Disputed Pokémon

While the Substitute doll originally looked similar to Rhydon, the design evolved over time to a more neutral design. In Super Smash Bros. for Nintendo 3DS/Wii U, its trophy description points out that, while it looks and gets attacked like a Pokémon, it is not actually one. The doll has gone on to receive several pieces of merchandise, including its own plush doll and clothes.

Main article: Legendary beasts

It is said that the Legendary beasts Raikou, Entei, and Suicune were reincarnated by Ho-Oh after they died in the fire that burned down the Brass Tower. They were said to represent the lightning that struck the tower (Raikou), the fire that burned the tower down (Entei), and the rain that put it out (Suicune). While it is unknown in the games if these three were already a Raikou, Entei, and Suicune before they were revived, the Pokémon Generations short The Reawakening shows them as three nameless Pokémon.

According to interviews with Ken Sugimori in Nintendo Dream, the bones that Vullaby and Mandibuzz wear are those of other Pokémon. However, it is not stated which Pokémon they are from, but they bear a notable resemblance to a human skull.

Pokédex entries say that most of the bones Mandibuzz uses to decorate its nest come from Cubone. These bones could also take part in Vullaby and Mandibuzz's design.

Main article: Tao trio

According to legend, Reshiram and Zekrom were once a single powerful dragon Pokémon used by twin heroes in order to create the Unova region. However, the brothers each sought something different in life—truth for the older brother and ideals for the younger—and they began to argue, then fight, over whose side was right. The single dragon, in response, split into two Pokémon: Reshiram, who sided with the older twin, and Zekrom, who sided with the younger twin. It is revealed in Pokémon Black 2 and White 2 that when the original dragon split into Reshiram and Zekrom, a third dragon, Kyurem, was "created" from the leftovers. The Pokédex entry for Kyurem also states that it is waiting for a hero to fill in the missing parts of its body with "truth or ideals". Kyurem can be fused with Reshiram or Zekrom to form White Kyurem or Black Kyurem, respectively, using the DNA Splicers, but the appearance of the original dragon Pokémon's complete form is unknown. In The Lesson Ends Here, the Original Dragon is briefly seen as a winged silhouette alongside the two heroes.

In Pokémon Sword and Shield, there are four types of Fossils, all of which appear to be incomplete, as they consist only of either a top half or a bottom half. Cara Liss can combine two Fossils that are opposite halves into one Pokémon, allowing half of the original prehistoric Pokémon to be seen.

• The Fossilized Drake, which forms the bottom halves of Dracozolt and Dracovish, appears to be from a heavy, spiked, dinosaur-like Dragon-type Pokémon.
• The Fossilized Dino, which forms the bottom halves of Arctozolt and Arctovish, appears to be from an Ice-type marine Pokémon.
• The Fossilized Bird, which forms the top halves of Dracozolt and Arctozolt, appears to be from a light, bird-like Electric-type Pokémon.
• The Fossilized Fish, which forms the top halves of Dracovish and Arctovish, appears to be from a marine, placoderm-like Water-type Pokémon.

However, the Pokédex entries for all four of the Generation VIII Fossil Pokémon suggest that they lived in prehistoric times, as does Cara Liss upon reviving one of them, though this information is somewhat implied to be inaccurate.

Main article: Arceus (Pokémon)

Arceus's conversation with the player after it is defeated in Legends: Arceus, heavily implies that the physical, goat-like form first seen in Pokémon Diamond and Pearl is not the actual Arceus, but only a piece of its whole being. In Legends: Arceus's opening scene, Arceus speaks to the player in its home dimension: there, it appears as a large amount of bright golden energy shaped like its main form. This unknown form may be Arceus's true appearance.

In the Scarlet Book in Pokémon Scarlet, a sketch of an imaginary Pokémon inspired by the Paradox Pokémon found in Area Zero is seen, drawn by a member of the Area Zero Expedition team. This Pokémon resembles the Legendary beasts: Raikou, Entei, and Suicune and their ancient counterparts: Walking Wake, Gouging Fire and Raging Bolt.

It's implied that this sketch was drawn by a member of the Area Zero Expedition team that managed to catch a glimpse of each of the Paradox Pokémon, Walking Wake, Gouging Fire and Raging Bolt during their exploration in Area Zero.

In the Violet Book in Pokémon Violet, a sketch of an imaginary Pokémon inspired by the Paradox Pokémon found in Area Zero is seen, drawn by a member of the Area Zero Expedition team. This Pokémon resembles the Swords of Justice: Cobalion, Terrakion, and Virizion and their futuristic counterparts: Iron Leaves, Iron Boulder and Iron Crown.

It's implied that this sketch was drawn by a member of the Area Zero Expedition team that managed to catch a glimpse of each of the Paradox Pokémon, Iron Leaves, Iron Boulder and Iron Crown during their exploration in Area Zero.

Main article: Loyal Three

In Kitakami myths, it is said that the Pokémon that formed the Loyal Three were once below-average Pokémon: Okidogi was small and weak, Munkidori was clumsy and dim-witted, and Fezandipiti had short, dull feathers. The Toxic Chains wrapped around their bodies granted them the strength, cleverness, and beauty that they respectively wished for. It's later revealed that Pecharunt was the one that transformed the trio with its Toxic Chains, while also using its Binding Mochi to tame them, so they could help it complete its journey to steal a brilliant set of masks desired by its caretakers.

The trio's original appearance is currently unknown and their Typings are implied to be completely different from the ones they now possess. What appear to be their original forms are depicted alongside a human child on Kitakami's signboards.

In The Ghost of Maiden's Peak, a Gastly with the ability to create illusions solid enough to attack people created a crossbreed of a Blastoise and a Venusaur, calling it a "Venustoise" (Japanese: フシギックス Fushigix).

Depicted in [{Ep163|Fossil Fools]], is the only representation in Pokémon the Series, albeit in statue form, of the aquatic life that Kabutops is said to have feasted on in most Pokédex entries since Pokémon Red and Blue.

Kabutops and the fish first appeared in art from the Pocket Monsters Encyclopedia, and bears some similarities to the silhouette on the Neo Genesis card Super Rod.

This clay artifact that looks like a Pokémon appeared in Fossil Fools and then again over nine-and-a-half years later in Bucking the Treasure Trend!. Professor Oak descibes it as an "ancient Pokémon fossil [or] artifact".

It is similar to the Clay Doll Pokémon Baltoy and Claydol and thus may have been based on shakōki-dogū, clay figurines from the Jōmon period of Japanese history.

In a sequence in Enlighten Up! where the main characters see their dreams for the future, Misty sees herself chasing an unknown "legendary water Pokémon". The only part of the Pokémon the viewer sees is a giant fin, which is reminiscent to that of the then-unreleased Mega Gyarados.

Main article: Unown (Pokémon)

Unidentified Unown seen on Professor Oak's computer in Spell of the Unown: Entei. Due to the introduction of two additional Unown forms in Generation III, some fans have speculated that these may have been very early prototypes for new forms of Unown. Some of the Unown resemble various Greek and Cyrillic letters, namely Я, Ω, Σ, б, Д, ω, Π, and σ.

An unnamed fairy was seen in Molly Hale's book of Legendary Pokémon in Spell of the Unown: Entei. It has some similarities to Beautifly.

An unnamed sun was seen in Molly Hale's book of Legendary Pokémon in Spell of the Unown: Entei. The only known Legendary Pokémon related to the sun is Solgaleo.

In Malice In Wonderland!, a wild Mismagius created an illusory Rayquaza belonging to the fake Cynthia. When Ash and his friends discovered that it was all just an illusion, it combined itself with its Rayquaza illusion.

In the first episode of Pokémon Origins, File 1:Red, an unknown cat-like creature with draconic wings appears briefly in Brock's Gym during the first episode.

In Play Misty for Me, there are a number of unidentified Water-type Pokémon at the Cerulean Gym. One of the most notable is a baleen whale-like Pokémon seen in the aquarium. It has three sets of flippers, coincidentally making it appear very similar to the much-later introduced Wailord. Others include a jellyfish, a fish located just underneath the jellyfish, and others swimming around the glass.

Main article: Thu-Fi-Zer

Thu-Fi-Zer (サ・ファイ・ザー Thu-Fi-Zer) was the result of a Team Rocket experiment created by fusing the three legendary birds—Articuno, Zapdos, and Moltres—in the Pokémon Adventures manga.

In-game image of the Eterna City statue edited to show the different interpretations of its design

In the Pokémon Adventures manga, first appearing in Ring Around the Roserade 1, the statue in Eterna City is neither Dialga or Palkia but a combination of the two statues. This is a reflection of the statue's appearance in Pokémon Diamond and Pearl and Pokémon Platinum being ambiguously shaped, in order to represent a different member of the duo in each game with a different tile palette. In Pokémon Brilliant Diamond and Shining Pearl, the statue was redesigned to be an explicit fusion between the two, similarly to how it appears in the manga.

After seeing the two Pokémon for the first time in Spear Pillar, Pearl theorized that the statue could represent how ancient people saw the two Pokémon fighting inside a distortion of space and time which led them to believe it was one Pokémon.

On the cover of the first chapter Introducing the Pokémon Clefairy!!, Red is shown surrounded by three stylized and mostly identical butterfly-like creatures with different patterns on their wings. Their overall shape and coloration gimmick quite noticeably resemble that of Vivillon.

Ten unidentified Pokémon are shown on page 21 of Introducing the Pokémon Clefairy!! where Clefairy accidentally destroys Professor Oak's lab. One of them resembles Slowbro with Gligar's head, while the others either have too few similarities with any known Pokémon or seems to have features of many different Pokémon.

This unknown Pokémon was captured by Red in The Big Battle In The Viridian Forest!!. It was his second Pokémon, after Clefairy. It is never named and the only other thing known about this Pokémon is that it is supposedly very weak. It escaped from its Poké Ball in the same chapter. Although it is commonly seen as a Bug-type by the fandom, it is most likely a really off-model Diglett as later representations of Diglett by Anakubo seem to confirm.

The Pocket Monsters Encyclopedia makes reference to Baby Nidoran, which were later seen on a 1997 ad for Pokémon Battoen.

Main article: MechaMew2

MechaMew2 is a Robotic Pokémon seen only in Pokémon Live!. It is considered by its creator Giovanni to be the most powerful Pokémon in existence. Giovanni promised Trainers the very rare Diamond Badge to anyone who could defeat it. MechaMew2 is based on Mewtwo, another Pokémon whose creation was ordered by Giovanni. It destroys itself at the end of the show after learning an attack of love, caring, and friendship.