- Entei (roaming Johto)
- Raikou (roaming Johto)
- Suicune (Tin Tower)
- Ho-Oh (Tin Tower)
- Lugia (Whirl Islands)
- Celebi (Ilex Forest)
Celebi is only obtainable through normal gameplay when the player has the GS Ball. Without events, this can only happen on Japanese or Virtual Console versions of Crystal; the latter is now impossible to obtain legally due to the closure of the eShop.
Articuno, Zapdos, Moltres, Mewtwo, and Mew were available in long-expired events that can no longer be legitimately accessed. The six Pokémon mentioned above are the only Legendaries available to players now.