What we know is that Yamamoto has been the Captain-commander for 1000 years. Yamamoto explained this in chapter 394. In addition, the Bleach Official Character Book SOULs, states that he founded the Gotei 13. He also founded the Shinō Academy 2,100 years ago. This is all we know. However it was stated that the location of the oken, the kings key, was passed down from one captain-commander to the next through word of mouth, so this would suggest that he was not the first.