It is not known to evolve into or from any other Pokémon, but it has the unusual ability to breed, despite being a Mythical Pokémon. It is also unusual in that its offspring are Phione, which do not evolve into Manaphy, and that Manaphy Eggs have a different appearance from other Pokémon Eggs.
Manaphy is a small, blue, aquatic Pokémon with stubby feet and club-like arms that are longer than its body. It has a red gem on its chest and a yellow dot below the gem. Its onion-shaped head has a pair of long blue antennae, which have small spheres on the ends. Its irises are dark blue with yellow sclerae, and there are two yellow dots of "eyelash" markings extending from the eyes.
Eighty percent of Manaphy's body is made of water. It is highly susceptible to its environment and swims long distances to return to its birthplace. Manaphy is known to live the Sea, specially cold seafloor. It has been known to rarely visit the costal waters of Hisui, occasionally with Phione following it. It is born with a special power that allows it to bond with any Pokémon. Manaphy can switch the perspective of people, and Pokémon, with each other using its former signature move, Heart Swap. Manaphy has been referred to as Prince of the Sea. As seen in the anime, Manaphy is capable of learning and speaking the human language. Manaphy is capable of creating Phione. Despite resembling Phione, the connection between the two is unknown at this point.
A Manaphy appeared in PMDP11, where Red and his Pokémon found it at sea. Professor Oak investigated it and told the group about the Egg hatching into a Legendary Pokémon. It later hatched into Manaphy but became lazy due to Clefairy's parenting skills.
When released from a Poké Ball, Manaphy uses Heart Swap, which temporarily switches the body of the user with another player. KO's count for the player in control, not the character's normal player, preventing easy KOs via suicide.
"A Seafaring Pokémon. Eighty percent of its body is made of water. It has the ability Hydration, which allows it to restore status effects at the end of the turn if it's raining. It is the only Pokémon who can use the stat-effect-swapping move called Heart Swap. Place a Manaphy and a Ditto in the Pokémon Day Care, and they will produce a Phione egg."
Manaphy appears as an occasional stage hazard in the Flood Chamber of the Kalos Pokémon League stage. Appearing rarely, it will use Whirlpool to create a maelstrom on the floor of the stage, sucking in any fighters standing in the water in an attempt to KO them.
This Water-type Pokémon is said to have the mysterious ability to bond with any other Pokémon. It's also said to appear occasionally in the Water-type Elite Four Trainer's room in the Kalos Pokémon League stage. When it appears on the stage, it'll use its Whirlpool move to drag fighters into the middle of the swirling waters.
Like the majority of Event Pokémon obtained through Mystery Gift, it was intended to be impossible to obtain a Shiny Manaphy. However, an oversight in Generation IV allows a Manaphy Egg to have a chance to hatch Shiny, but only if it was traded before hatching. This is because Shininess is dependent on the Trainer ID number and Secret ID number, and the game mistakenly attempts to prevent Shininess using the original game's ID numbers instead of the ID numbers of the game that it was traded to. This oversight was undone by the time Manaphy's Egg returned in Generation VIII. Shiny Manaphy that are hatched from a traded Egg can still pass Poké Transporter's legality check.
Manaphy's trait of only being able to produce Phione as offspring may be inspired by eusociality, a biological phenomenon which usually manifests in a colony of animals having a sole breeding female, or queen, tended to by her usually infertile offspring, or an example of a highly rare and unique mutations such albinism or polydactyly. With Manaphy's title as the "Prince[ss] of the Sea" and Phione's unclear status as Mythical, it may also take influence from the illegitimate children of royalty and nobility, whose worthiness to inherit their parents' status is often disputed.
Manaphy may be a combination of mana (spiritual life force in Polynesian culture) and fay (fairy).