How do we know? I'm not entirely sure... I'm FtM, but I figure the feelings are parallel and the reasons related; I mean, how different can we really be in terms of biology - brothers and sisters under a trans umbrella?
I guess the best way I could explain it (in my point of view) is the identification with my dad. When I was younger, it was always me and him against the world. No question that I'd grow up to be just like him, at least, until I realized things just don't work like that. I mean, I've always felt... different as a kid. I couldn't exactly pinpoint what separated me from the rest, but I distinctly remember the feeling. Didn't want to play with the girls and the boys didn't want to play with me, so I just kinda did my own thing. Made friends with a few girls later on, but we never played any gender specified games. They were there because they felt bad for me, initially, but grew close over the years. The lot of us were tomboys, I guess you could say, but the problem was that once we all reached puberty, they grew out of it and I... didn't. Suddenly, they weren't just my friends who were girls, they were GIRLS who were my friends.
It was around this time that I began to regress, and fought growing up as hard as I could. I hated the idea of my body maturing like the other girls and it was almost torture to see my female friends go through puberty first and think "That won't happen to me, right?" It was only months before I caught up with them, and longed for the pre-pubescent days. I went through a brief stage of regression during that time, finding all sorts of reasons why I shouldn't grow up, while also finding reasons to believe that I was actually a guy. "Got over it" around the age of fifteen after my parents demanded that I learn some responsibility, and so began my "girl phase" where I tried to fit in. That didn't really go over well, since I was torn half the time. Being generally secluded made any social gatherings particularly exciting, but the prospect of wearing clothes I detested made me stay home more often than not. Around last year, I picked up a sort of "who cares" attitude when it came to my appearance, and also got into writing and role playing. It was through writing that I came to terms with myself and came up with the easiest explanation for why I feel like I'm a guy:
When I wrote for a girl character, I always wrote in the third person, which focused more on detail in surroundings and events rather than thought. When I wrote for a guy character, I wrote in the first person and just let my thoughts fill up the page. The detail was still there, but the writing felt more... personal. More me.