Board Thread:General Discussion/@comment-93.186.153.226-20140505211822/@comment-3131736-20150411175625

In a radio-conversation, Sigint explains that Ocelot was born on the battlefield and that he had to be cut out of his mother's womb, leaving her with a big scar on her body that looked like a snake.

And before their final battle, The Boss shows Big Boss her scar so it's absolutely 100% confirmed that Ocelot is the Boss's son.