I beleive that it will be the one you first see. Like when you see a Spinda in R/S/E, the pattern of spots of the first one you see will be the same in the Pokedex.
Maybe in the pokedex the first picture that comes up is the gender you first saw. But probably when you can check its cry or whatever,you can also see the female or male version of the pokemon.
I beleive that it will be the one you first see. Like when you see a Spinda in R/S/E, the pattern of spots of the first one you see will be the same in the Pokedex.