Between Omega Ruby and Alpha Sapphire, there are dozens of legendary Pokémon—not all of which are easy to find. But if you're set on hunting them down, you've come to the right place.
First thing's first. Hunting for many of these Pokémon becomes easier after you've beat the game. That's because, as you may know, legendary Pokémon are tough to capture. It can be a time consuming, money intensive task. It's not unusual to spend more than 20 ultra balls on a single legendary, if not more. You could go broke trying to capture these Pokémon, thanks to how many Pokeballs you'll have to buy in total. If you have nothing pending, it's easier to spend time simply grinding money with the purposes of capturing more legendary Pokémon.
Aside from money, keep in mind that legendary Pokémon are usually strong. Should you go and try to capture a legendary, you have to make sure to bring a team of formidable Pokémon—but nothing too strong, because you don't want to one hit KO your target. I'd suggest a team in the 50-60 range—most legendaries appear at around 40-50, with the exception of Deoxys, that is a whopping level 80.
Beyond that, it's worth reiterating how to capture Pokémon. Here, I'll quote Bulbapedia, since it's illuminating:
The probability of catching a Pokémon starts with the species' catch rate divided by 255. Then it is multiplied by the following factors:
The health of the Pokémon (relative to its full health), which can reduce the probability to ⅓× at full health.
The type of Poké Ball, which can augment by some ×.
Any status condition of the wild Pokémon (i.e. 2.5× increase for sleep or freeze, and 1.5× for paralyze, poison, or burn).
Any active Pass Powers (in Generation V) or O-Power (in Generation VI).
The effects stack multiplicatively—for example, a 2× and a 3× will combine to be 6×. If the calculation ends up greater than 1, the wild Pokémon is assured to be caught.
The rarity of the Pokémon (i.e. how often it appears in the wild) is totally independent from its catch rate after it is encountered.
In simpler terms: the more damage you deal to a Pokémon, the easier it is to catch. Status conditions, as well as Pokeball types, can help—so if a Pokémon is in the red and asleep, they're more likely to be captured by an Ultra Ball than an awake Pokémon in the yellow. And finally, don't forget about O-Powers, which you can use to grant yourself a tiny boost in capturing effectiveness. You can find O-Powers buried in the PSS, after hitting the folder icon, and then going into the second menu. Even with all that information and preparation, it can be tough to capture a legendary—but every little bit helps.
Now that we've got all the planning stuff out of the way, let's talk Pokémon! Most of these, I have either caught myself, or have gotten tips from friends that have captured them. Occasionally, I'll cite Serebii, an informational Pokémon website.
Kyogre and Groudon
These are likely the first legendary Pokémon you'll capture, since they're a part of the story. Right before the last gym, you'll be pulled into one final bit with whatever evil team exists in your version of the game. Since the villain's plan involves reviving either Kyogre and Groudon, you'll end up right in battle against these legendaries if you play through the story enough. I'd suggest sticking to ultra balls for this one. They're only level 45, it shouldn't be that tough. You'll get whatever legendary is on the cover of your game.
Worth capturing because: they're the only Pokémon that have a primal form, for now.
Latias and Latios
A level 30 Latias or Latios holding their respective mega stone will be given to you by Steven if you play through the story. You should get them around the same time as Groudon or Kyogre, and thankfully, you don't actually have to capture them. The game just gifts them to you! Nice.
Worth using because: you can use the Eon Flute, which lets you fly around in the sky. It's a cool feature, but more importantly, it lets you capture other legendary Pokémon. So don't release Latias or Latios, whatever you do.
Rayquaza and Deoxys
I'm grouping these together, not because they're related, really, but only because the game makes you fight one after the other. After you beat the game, you'll have the option to do a special "Delta Episode." The episode takes an hour and a half to complete at most, and at the end, you'll go into battle against a level 70 Rayquaza. Once you capture it, you'll throw it in your party per the story's request, and go up against Deoxys.
Both of these Pokémon are tough to capture, but if you must use a Master Ball on one of them, I'd recommend Deoxys, simply because it's the highest level legendary available. It took me about 6 different tries to capture Rayquaza, so I'd come prepared.
Worth capturing because: Rayquaza gets the coolest mega evolution in the game, and Deoxys is probably the rarest available legendary in ORAS.
One of the easier legendaries to find, Heatran was the first non-story related legendary I caught in my game. You can find him at the bottom of a place called the "Scorched Slab," right after you capture Groudon and Kyogre. When you get to the part of the cave with a weird, floating ring, go up to it, press A, and you'll be transported to a level 50 Heatran. Because, uh, magic.
Worth capturing because: he's easy to find.
Solving The Big Puzzle
Now, for the next three, you're going to have to some tricky maneuvering, as well as some puzzle solving. First, you'll want to visit Pacifidlog Town, one of the only places without a gym. You'll find it to the left of Sootopolis City. Once you get to Pacifidlog Town, go as far left as you can, and start surfing. You'll note that the map will be full of rapid currents, which make it impossible to navigate the water freely. Don't worry about it for now. Just keep going left, letting the water take you wherever it will, until you end up at the edge of the town of Slateport.
Now fly to route 133, and once your Pokémon sets you down, take this specific route:
Basically, you're trying to get to a small dive spot in the middle of route 134, except it's covered by fast current. This is the only pathway you can take to get right on the patch. Unfortunately if you fly right to route 134, your Pokémon will drop you off somewhere where you can't reach the dive spot, which is why I suggest flying to route 133. It's easier than trying to figure out where the exact route starts at 132.
Anyway, once you get to the spot, dive, swim until you get to a cave, and surface. There, you'll find a cave full of Braille. If you want to solve its secret message on your own, you can. But if you don't want to do that, here's the solution: go up to the message on the top, as I show in the video, and use dig. The door to the next room should open. It's already open in my video because I've already done this before, but it won't be in yours.
In the next room, you'll want to place a Relicanth as the first Pokémon in your party, and a Wailord as the sixth Pokémon in your party. You can find a Wailmer around Sootopolis if you're having trouble—use the DexNav so that you ensure that the only Pokémon that appear are Wailmers. Then, level that Wailmer to level 40, at which point you'll have a Wailord. Excellent. Relicanth, on the other hand, can be captured if you dive around Sootopolis. Once again, it's easier if you use the DexNav to capture it.
With both those Pokémon in-hand, go up to the second room's message at the top, and read it. That should trigger an event that opens up a few caves around the map—you may have come across them before while exploring, only they had no entrance at the time. Now, because you did all this stuff inside this ~secret sealed chamber~, they do. Let's go by the Pokémon this unlocks one by one, shall we?
You'll find this one at level 40 on route 105, north of Dewford town. Go into the cave, read the message, and wait for two minutes. A door will open, and you'll find Regice.
Important note: nickname it something after you capture it. I know this sounds weird, but trust me. We'll get to why later in this guide.
Why you should capture it: Regice, along with its 'brothers,' are some of the most fun legendaries to capture, thanks to all the puzzles surrounding them.
You know that desert in route 111, with the perpetual sandstorm? Somewhere near the bottom of that desert, there's a cave you can go inside. And inside that cave is a level 40 Regirock. According to Serebii, after reading the message inside, you need to "go right twice, down twice (best use the D-Pad for this) and then use Strength and the door to Regirock should appear."
Why you should capture it: You captured its brother. Why not get this one, too?
Possibly the coolest of the Regis, a level 40 Registeel can be found right of Fortree City, on route 120. You'll need surf, though. Once inside the cave, read the message, and go to the middle of the room and use fly. Voila: Registeel!
Why you should capture it: You need all three Regi 'mon if you want to get the next legendary.
This one is a doozy, and is also the entire reason why you captured all the Regis before it. Behold, Regigigas, a Pokémon that sort of fuses all the Regi golems. In order to find it, you need to talk to someone and then be at the right place. Serebii explains, "In Pacifidlog Town, in the north-eastern house, a girl will tell you stories her grandfather told her. At random, she will tell you a part of the story about how to get Regigigas. This involves location and the other features. Take all three of the [Regis] to the Island Cave."
For whatever reason, encountering Regigigas requires you not just to have all three Regis, but to have a nicknamed Regice holding one of three items: CasteliaCone, Snowball or Never-Melt Ice. If you do all this right, when you enter Island Cave, you should hear an earthquake, and then Regigigas will challenge you. Neat, eh?
Why you should capture it: It's the motherlode, as far as Regi Pokémon are concerned—and if you went through the trouble of capturing all the other ones, why not this one, too?
Uxie, Mesprit, Azelf
The next three, like Heatran, are a bit easy to encounter.
As you might recall, using the Eon Ticket with Latias or Latios allows you to fly around the overworld map. While soaring, you might come across special islands, which aren't normally locations on your map—like say, something called "Nameless Cavern." It might look a little bit like this:
Land on it, go inside the cave, and go inside the portal. You'll encounter one of the three level 50 Pokemon at random. Just one at a time, though. The special glowing orb containing one of these three Pokemon will replenish/reappear again after twelve hours, so make sure to soar again later in search of these.
Why you should capture them: The bringer of emotion, the bringer of knowledge, and the bringer of willpower. These legendaries have a neat concept, no?
Lugia and Ho-Oh
These ones are fun. If you explore Sea Mauville, which is right near Slateport…
...you get the feeling that the shipwreck is hiding something—and it is. Lots of things, in fact. At Sea Mauville, not only do you get some interesting (but sad) Pokémon lore, you also have the chance to capture the big legendaries from Gold and Silver, Lugia and Ho-Oh. Lugia is exclusive to Alpha Sapphire, whereas Ho-Oh can be found in copies of Omega Ruby. Both will be level 50.
To capture them, you're going to need to find a scanner. To find the scanner, you need to enter the ship, surf on the water, and then dive down to the deepest level on the ship. You'll know you're there because it'll seem like an empty basement. It's not empty, though. On the right side of the stairs, if you press A at the exact right spot, you'll find an invisible item—the scanner. I found it here, if you need some visual guidance:
On my Alpha Sapphire copy, I didn't find it in the exact same spot, but rather a couple of tiles over—so don't be afraid to mash A in the general area, because that's the only way you can pick this item up.
Once you have it, head on over to Slateport, and find the Slateport Harbor. Captain Stern should be inside, and he'll trade you the scanner for one of two items. In Omega Ruby, you'll get the Clear Bell that summons Ho-Oh. In Alpha Sapphire, you'll get the Tidal Bell, which summons Lugia.
If you have the Clear Bell, you need to head back to Sea Mauville, and go as far up on the outside of the ship as you can. Once you reach the edge of the deck, you should see a portal. Inside that Portal is Ho-Oh.
Lugia, meanwhile, can be found in the basement of Sea Mauville, right near where you found the scanner. You just have to make sure to bring the Tidal Bell with you.
Why you should capture them: Sea Mauville is worth exploring on its own—so while you're there, why not capture some legendaries, too?
Suicune, Raikou, and Entei
If you have both Lugia and Ho-Oh on your team, you should be able to find the three level fifty legendary dogs while using the Eon Flute. They'll be inside a special location named "Trackless Forest." This forest, as you may have guessed by now, has a portal—and this portal will take you to one of the three legendary Pokémon. According to Serebii, in order to get all three, you need to "remove the Pokémon [you captured] from your team and then readd them again to get the next one."
Why you should capture them: they're probably the cutest of all the legendaries here, and if you captured Lugia and Ho-Oh, why not get the Pokémon they unlock, too?
Cobalion, Terrakion, Virizion
Like Uxie, Mesprit, and Azelf, these three Pokémon can be captured in one specific type of location: the Pathless Plain. You'll find it near Pacifidlog Town, while using the Eon Flute. Land on the Pathless Plain, go inside the portal, and you should find one of three legendaries there—all level fifty. Once you capture one, if you wait twelve hours, you can capture the other two in fresh Pathless Plains, too.
Why you should capture them: They're easy to find, and they're based on The Three Musketeers. What's not to love?
Palkia, Dialga and Giratina
Palkia and Dialga are version exclusives—Omega Ruby for Palkia, and Alpha Sapphire for Dialga. You'll find them at level fifty if you use the Eon Flute—but only if you already have Uxie, Mesprit, and Azelf. If you have them equipped, somewhere around Dewford town you should be able to find a weird green rip in the sky while soaring. Yes, you can enter it—inside you'll find your version exclusive, depending on what game you own.
That gives you one Pokémon. But in order to get Giratina, you'll need both Dialga and Palkia in your party, which means you're going to have to do some trading. Once you have both legendaries equipped, using the Eon Flute near Dewford should bring up another tear in the sky—this time, it'll contain a level fifty Giratina.
Why you should capture them: according to Pokémon lore, these three Pokémon helped create the world. They're like god Pokémon. That, and if you went through the trouble of collecting Uxie, Mesprit, and Azelf, why not get the legendaries that they unlock, too?
Reshiram, Zekrom, Kyurem
These two are also version exclusives—in Omega Ruby, you'll find Reshiram, and in Alpha Sapphire, you'll find Zekrom. To pin these down, you need to use the Eon Flute and soar around until you find a red bundle of light, which should lead you to a "Fabled Cave." Once you land, you should find a cave and a portal that should take you to your respective level fifty legendary. So many portals!
Like Giratina, Kyurem is only capturable if you already have two other Pokémon in your party. In this case, Reshiram and Zekrom. Once again, you'll have to do some trading to get this to work, since they're both version exclusive.
Once you have both Pokémon in your party, you should find an area called the "Gnarled Den" while using the Eon Flute. Inside, you'll find a portal that houses Kyurem. Serebii notes that you'll want to use the Dowsing Machine in the Gnarled Den too, as it'll reveal DNA Splicers, an item you can use with Kyurem to change its form.
Why you should capture them: They're dragon legendaries, and they're easy to find.
Tornadus, Thunderus, and Landorus
These three genie-like Pokémon are gods of weather, and so it shouldn't be surprising to hear that the way you acquire them involves the weather, too. At some point during the story, you'll have to go into the Weather Institute, where they'll gift you Castform. If you have Castform in your party while using the Eon Flute, you should find a thick, black cloud floating in the air somewhere on the map. If you get close to it, you'll get sucked into battle with Thunderus if you have Alpha Sapphire, and Tornadus if you have Omega Ruby. Both will be level fifty.
To get the final Pokémon, Landorus, you'll need both Tornadus and Thunderus in your party while using the Eon Flute. You'll find it in a black cloud, too.
Why you should capture them: They're genies, and they even have different forms. They're pretty awesome, for modern legendaries.
I haven't actually been able to find Cresselia in my game yet. Serebii itself notes that the unlock method for this legendary is unknown, but that apparently you can find it on an island near Ever Grande City at level fifty, on the other side of a portal (of course).
And...that's it. Those are the known legendary Pokémon that you can capture in Omega Ruby and Alpha Sapphire. While Game Freak promised you'd be able to capture every legendary in the franchise thus far, you may have noticed that this list doesn't include all of them. Where are Pokémon like Mewtwo and Mew, for example? I'm not sure if some Pokémon are omissions, or if we just haven't figured out how to find them yet. Either is possible, and I'll update this guide should anything change.
For now, there are still a ton of legendaries for you to hunt. So go out there, grab some Pokeballs, and get to capturing 'em.