Some enemies are not members of any known biological family. These enemies are shown as being in the Unknown family in Pikmin 2 and Pikmin 3 Deluxe, ? family in Hey! Pikmin, and ??? family in Pikmin 4. Most of these enemies seem to have no biological relationship, despite many of them sharing similar traits or names.
- Main article: Ancient Sirehound.
The Ancient Sirehound is the final boss of Pikmin 4. It is a green and blue space dog and is implied to be controlled by Louie. It has multiple phases based around different types of hazards seen in the game.
Berserk Leech Hydroe
- Main article: Berserk Leech Hydroe.
The Berserk Leech Hydroe is the final boss of Hey! Pikmin. It is a gigantic plant creature, it has a purple and white body with grass and some sprouts growing on its back. It has three stalks with very few and small spines and Venus flytrap-like mouths on the ends, the central one being larger and acting like the main head while the smaller ones are used as its primary method of attack. In its second phase it can come out from the ground revealing that it has 4 brown legs with clawed feet. After defeating the second phase the creature's body withers and the central head detaches from the dead body retaining a small portion of it. This new body sprouts wings and has smaller feet lighter in coloration than the ones from the main body.
- Main article: Fireflinger Groink.
The Fireflinger Groink is an enemy that appears in Hey! Pikmin. Although it is never stated they are related, the Fireflinger Groink shares many similarities to the Gatling Groink, which is interesting since both creatures do not belong to any known family.
- Main article: Gatling Groink.
The Gatling Groink is an enemy in Pikmin 2. It is a large biomechanical creature with eyes staring forward, two legs, a mechanical tail and a mouthplate that is opened to fire mortar rounds. Despite not having a very dangerous attack, it possesses strong defensive capabilities and is often located in hard-to-reach places, such as on top of pillars, increasing its protection against Pikmin even more. It attacks by initiating a cannon from its mouth and fires 3 mortars at regular intervals when in range of a target. When the balls hit the ground, they scatter all Pikmin in range and kill those at the absolute center of the blast. The method to attack it is to throw Pikmin at its rear, where it lacks metal shielding. It can shake the Pikmin off when agitated, and unlike most enemies, the shaking occurs without any visible preparations, giving the player hardly any reaction time. Because Purple Pikmin stun when they land on the ground, it is not necessary to get behind it to immobilize it with purples. Once killed, it starts regenerating health, making it crucial to carry it to an Onion or the Research Pod. If it isn't carried back on time, it will revive and continue its attack.
- Main article: Glow Pikmin.
Glow Pikmin are a type of Pikmin that can only be used at night during night expeditions, and in caves. Glow Pikmin have bright green, bioluminescent bodies. They have no legs; their bodies instead end in a tapered and ghost-like tail. Because of this, they have the ability to float. They have blue eyes, though one of them appears to be larger than the other and has a light blue pupil. Their flowers are also slightly differently shaped, with five pointed petals (resembling a star) instead of the normal rounded ones. They also appear to be slightly smaller than other Pikmin types.
- Main article: Lumiknoll.
Lumiknolls are large dirt mound nests found in night expeditions in Pikmin 4. They are the home to Glow Pikmin, and function similarly to the Onion, although their behavior is quite different. Lumiknolls produce Glow Pikmin when fed with glow pellets. Juvenile Lumiknolls, known as Tricknolls, are also found within night expeditions and serve as an extension of the Lumiknoll.
- Main article: Moss.
Moss is a space dog in Pikmin 4. In the game's prologue she is found by Captain Olimar when he crash-lands on PNF-404 and quickly befriends him, helping him throughout his search for his ship's missing ship parts. After the prologue, Moss is seen accompanied by a leafling-transformed Olimar, and accompanies him during Dandori Battles.
- Main article: Plasm Wraith.
The Plasm Wraith is the final boss of Pikmin 3. It is a gold-covered wraith that can assume multiple forms and is relentless in its desire to capture and keep Olimar under its care. It can use a flurry of stabbing attacks to eat Pikmin that aren't Rock Pikmin and can spit out Elemental Plasms for fire, electricity, water, and crystal, destructible by the Pikmin type that is resistant to the relevant element.
- Main article: Ujadani.
Ujadani are small, rare creatures from Pikmin 2. They only appear in Wistful Wild every 30 days from day 31 onwards, and can be found around the Hole of Heroes and Dream Den. They will ignore leaders but will immediately swarm Pikmin and occasionally release poison. Pikmin will attack them of their own accord, but when attacked the Ujadani will not only release poison but also nectar or sprays. They are not documented in the Piklopedia, so the information about them belonging to an unknown family is only seen on their e-Reader e-card.
- Main article: Waterwraith.
The Waterwraith is a watery, humanoid boss in Pikmin 2 and Pikmin 4. It appears to have a human shape, a head, body, arms, and legs, without distinct characteristics though, since it is transparent. It falls from the sky and moves around on stony rollers, chasing leaders and their Pikmin. It is invincible to any Pikmin assault, even if petrified, except when attacked by Purple Pikmin. When a Purple Pikmin lands on or near the Waterwraith, it turns dark and becomes vulnerable to all Pikmin attacks. When the player depletes its health, the rollers crumble and the Waterwraith will run around the cave until defeated.
Unknown 'mamuta' family
Although the Piklopedia shows the Mamuta and Smoky Progg as having an unknown family, multiple Piklopedia comments for the Smoky Progg state that it is a malformed larval Mamuta, and as such, are the only enemies categorized under 'unknown' to have a confirmed biological relationship.
- Main article: Mamuta.
The Mamuta is an enemy found in Pikmin, Pikmin 2 and Pikmin 4. It appears rocky, with two small eyes and two arms of dissimilar size. In the both Pikmin and Pikmin 4, it will just stand and watch any Pikmin walk by. Any attack on it, however, causes it to become enraged and pound the Pikmin into the ground. This, strangely enough, doesn't kill them but will replant them and turn them into flower Pikmin. In Pikmin 2, they are more aggressive than in the other games they appear in.
- Main article: Smoky Progg.
The Smoky Progg is a hidden boss in Pikmin and Pikmin 4, and is possibly one of the toughest. The only way to encounter it is to go into The Distant Spring area before day 15. It resides in the massive lake area, on a later useless mound of small islands, in an egg form. If one touches the egg by any means, even with Olimar, it will break out of the egg and show its true form; a dark green and black creature, emitting fumes toxic to Pikmin, sporting glowing white eyes. It will follow the player back to the landing site, so it's necessary to kill it. It can uproot Pikmin sprouts. The only way to hurt it is to throw Pikmin onto its large head. Any Pikmin left walking in its trail will succumb to the unknown substance it emits. It has an incredibly high defense and takes a while to kill. However, when killed it drops a pearl or nut that will be sufficient food to produce 100 Pikmin from any Onion that it gets to.
- Previously, this article also included species with unspecified families. Specifically, the five species from Pikmin (a game with no official creature log) who did not return for Pikmin 2. As of the release of Pikmin 4, all five of these species have received an official family in some capacity.
- While the adult Armored Cannon Beetle has yet to technically return, its younger variant, the Armored Cannon Larva, is classified in the Lithopod family.
- The Puffstool was assumed to be related to the Puffstalk from Hey! Pikmin, and assumed part of the same famliy, the Sporovid family. Pikmin 4 confirmed this to be true.
- Pearly Clamclamps returned in Pikmin 4 and were classified under their own family: the Snareshell family.
- The Smoky Progg was described as related to the Mamuta, who were confirmed to belong to an unknown family in Pikmin 2. Both returned in Pikmin 4 and confirmed them both to each still be in an unknown family.
- While the Goolix has yet to return, a similar creature named the Foolix appeared in Pikmin 4 and was classified under the Goolix family. As the family is named after the Goolix, it's assumed to belong to that family.