Anime involving a love story and two samurai/assassin villages, previously on unfriendly terms, that were made to fight each other again
This sounds a lot like Basilisk. 



There are two warring ninja clans, one led by a girl, Oboro Iga, and the other a man, Gennosuke Kouga, who are both secretly in love with each other. They all have unique supernatural powers. During the course of the story, Gennosuke is blinded by a spell of some sort and they both of to fight each other at the end of the series.

It's very much like a "Romeo/Juliet" type story set in 17th century Japan.

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