I was thinking about this myself. For male characters it's pretty obviously Mario, but for female characters, it's a bit harder since none of them are as popular as he is. I have some ideas though.
Lara Croft
Lara Croft has one of the most notable series with a female lead, and for a while I would have said she was the most popular. However, Tomb Raider's sales in proportion to the gaming industry has gone down a fair bit since the 90s.
Peach
If Mario is the most popular male character, the most popular female character in the series has got to be Peach. She is a central character in almost all the main Mario titles. However, I don't know if she herself would be consider the absolute most popular character.
Those are two ones I'd think of. I guess there may be others like Saber (King Arthur) or some personal ones that come to my mind (Chun-Li), but I don't know if either of them would be more popular than the two I already listed.
Lara Croft
Lara Croft has one of the most notable series with a female lead, and for a while I would have said she was the most popular. However, Tomb Raider's sales in proportion to the gaming industry has gone down a fair bit since the 90s.
Peach
If Mario is the most popular male character, the most popular female character in the series has got to be Peach. She is a central character in almost all the main Mario titles. However, I don't know if she herself would be consider the absolute most popular character.
Those are two ones I'd think of. I guess there may be others like Saber (King Arthur) or some personal ones that come to my mind (Chun-Li), but I don't know if either of them would be more popular than the two I already listed.