How do you breed legendary Pokemon?

Most Legendary Pokémon are incapable of breeding the only known Legendary Pokémon that is capable of breeding is Manaphy and it is capable of breeding in all main series games since its introduction into the main series of games in Pokémon Diamond and Pokémon Pearl however Manaphy can only breed with Ditto and the resulting egg will cause the egg to hatch into Phione which will not evolve or transform into Manaphy.

Only Manaphy can breed. You need to leave it in the Daycare with Ditto to get a Phione egg.