Legendary Trio

In each generation, there is typically at least one group of Legendary Pokémon that form a trio. Each Trio is seemingly subject to another Legendary Pokémon.

Generation I

 * Articuno, Zapdos and Moltres – The Legendary Birds, ruled by Lugia

Generation II

 * Suicune, Entei and Raikou – The Legendary Beasts, ruled by Ho-oh

Generation III

 * Regice, Regirock and Registeel – The Legendary Golems, ruled by Regigigas
 * Groudon, Kyogre and Rayquaza – The Weather Trio. The master of this trio may be Rayquaza, but it is unclear as to why the identity of the master is concealed.

Generation IV

 * Uxie, Azelf and Mesprit – The Lake Trio, ruled by Arceus.
 * Dialga, Palkia and Giratina – The Legendary Dragons, ruled by Arceus.

Pairs
Some of the remaining Legends fit into pairs, namely
 * Mewtwo and Mew
 * Ho-Oh and Lugia
 * Latios and Latias
 * Cresselia and Darkrai