Pokémon Crystal was the first main-series Pokémon title to let players choose a character’s gender.
Earlier main-series games presented the player character as a boy. Crystal, an enhanced version of Gold and Silver, added a female option alongside the established male protagonist. The choice affected the player character’s appearance and name, while the core adventure, region, and battle systems remained the same.
This was an important customization step for the series. Crystal also included animated Pokémon sprites, a more prominent story role for Suicune, and other changes that distinguished it from Gold and Silver. It retained the Johto and Kanto regions and the large collection of features introduced in Generation II.
Pokémon Emerald is sometimes given as the answer because it was another enhanced third version and is more familiar to some players. However, Emerald followed Crystal by several years. Pokémon Yellow also changed the starter and story presentation, but it did not offer a gender choice.