Board Thread:Improvements and Issues/@comment-5355747-20130313062554/@comment-11051098-20130710175528

I'd say we don't know if there is any main house AND branch house. I read it as Isshin at the time being the head of the whole clan, but even though he was from a branch family and not the main family, I'd say he could have been the head of the whole clan.

Of course it's just pure guessing how it really is.