Alphys (/ˈælfiːz/ AL-feez) is a female, reptilian monster that lives in the lab in western Hotland. She is the incumbent Royal Scientist, a position she was awarded by Asgore after the disappearance of her predecessor.

What gender is Alphys and Undyne?

Again, Alphys is female. There is no question about this. Every single character and the game itself refers to Alphys as "she." Yes, the fact that both Alphys and Undyne are female and are coupled together makes them a lesbian couple.

Is Undyne a boy?

Undyne is female, same as Alphys. There's nothing wrong with being lesbian in Undertale.