Rayquaza locations — where to catch

In Paldea (Scarlet & Violet)

• Inlet Grotto — Static Encounter

In Johto & Kanto (HeartGold & SoulSilver)

• Embedded Tower — Static Encounter

In Hoenn (Ruby, Sapphire & Emerald)

• Sky Pillar — Static Encounter

Other games (4)

• Mega Dimension (Gen 9): Sky Pillar
• Sword / Shield — The Isle of Armor (Gen 8): Max Lair
• Ultra Sun / Ultra Moon (Gen 7): Ultra Space Wilds, Ultra Space
• Omega Ruby / Alpha Sapphire (Gen 6): Sky Pillar

Rayquaza — full Pokédex entry