John Beiswenger, author of the novel Link (first published in 2003), has sued Ubisoft, claiming that the historical/sci-fi series infringes on a number of his copyrights.
Basically, he alleges that because his book involved a system which could access ancestral memories, then the fact Assassin's Creed also uses that as a cornerstone of its plot (along with secret research facilities and mentions of religion and creation) means it's cutting in on his turf.
Where Beiswenger may come undone is that he alleges Ubisoft "have directly copied, and
directly and contributorily infringed on the whole of Plaintiff's copyrighted work".
Now, similarities there may be between the two works, but that's art, baby. You build new stuff from the bones of the old. Even if anyone from Ubisoft had read Link, unless its plot is also about Templars vs Assassins and stars flamboyant Italians (which it doesn't), then it's not directly copying anything.
Interestingly, alongside practically every Ubisoft outpost, it seems GameTrailers has been roped into the lawsuit as well, for the heinous crime of showing this 2010 trailer...about PlayStation Home.