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Pokémon Crystal vs Gold & Silver: Every Difference

Crystal is the third version of Johto: the same regions, Gyms and League, but a new Suicune storyline, a female player, the Battle Tower, the Odd Egg and changed wild Pokémon. The Pokémon lists below are worked out by comparing every encounter table, gift, trade and prize in Crystal with the Gold and Silver data.

Missing from Crystal
10
Gold/Silver exclusives Crystal has
16

What changed

StorySuicune is the legendary at the heart of the story: it appears at the Burned Tower, in Cianwood City, on Route 42 and Route 36, and finally waits on Tin Tower 1F. Eusine, a Suicune hunter, is a new character, and the Wise Trio guard Tin Tower.
PlayerYou can play as a girl, Kris, for the first time in the series, or as the boy.
LegendariesHo-Oh and Lugia are both level 60 and both post-game: Ho-Oh needs the Rainbow Wing (after the Elite Four, once Raikou, Entei and Suicune are caught), Lugia needs the Silver Wing from Pewter City. In Gold and Silver one of them is level 40 and part of the story. Celebi has an event in Ilex Forest with the GS Ball.
New placesThe Battle Tower on Route 40, the Dragon Shrine in the Dragon’s Den, the Wise Trio’s room in Ecruteak and new rooms in the Ruins of Alph.
GiftsThe Odd Egg from the Day-Care, a Dratini that can know ExtremeSpeed from the Dragon Shrine, and Kurt’s Apricorn balls as before.
MovesA move tutor in Goldenrod teaches Flamethrower, Thunderbolt, Ice Beam for 4,000 coins each after the Hall of Fame.
Game CornersGoldenrod offers Abra, Cubone, Wobbuffet; Celadon offers Pikachu, Porygon, Larvitar.
Wild PokémonMany encounter tables changed, so several Pokémon from Gold and Silver are missing (below) and others moved to new routes or times of day.
PresentationPokémon play a short animation when they enter battle, and Crystal runs only on the Game Boy Color.

Pokémon you cannot get in Crystal

These 10 Pokémon can be caught, evolved or bred in Gold or Silver but not in Crystal; trade them in.

Gold and Silver version exclusives in Crystal

FAQ

Is Crystal better than Gold and Silver?

Crystal has more story, the Battle Tower, the Odd Egg, the move tutor and the female player, but misses a few Pokémon such as Mareep and Vulpix. Many players treat it as the definitive Johto game on the Game Boy Color.

What Pokémon are missing in Pokémon Crystal?

Vulpix, Ninetales, Mankey, Primeape, Mareep, Flaaffy, Ampharos, Girafarig, Remoraid, Octillery.

Can you trade between Crystal and Gold or Silver?

Yes. Crystal trades and battles with Gold and Silver directly, and with Red, Blue and Yellow through the Time Capsule.

Sources & picture credits

Guide text is original retrogameindex writing, checked against the game’s own scripts and Bulbapedia. Wild Pokémon and encounter chances for all three times of day, fishing, Headbutt and Rock Smash tables, items, trainers, gifts, trades and shops come from the pret/pokecrystal decompilation (pret/pokecrystal 3bc8daa417). Maps, sprites and the Johto and Kanto Pokégear maps are drawn by retrogameindex from the game’s own graphics in that decompilation (listed on the image gallery). Pokémon © Nintendo / Creatures / GAME FREAK.