Pokemon come in a variety of colors and forms, but generally, each species looks the same. The notable exception to this rule is shiny Pokemon, which feature unique color variations and are rarer to find in the games. Shiny Pokemon have also appeared in the anime, with Ash's Noctowl being the first example introduced in the Johto Journeys series, where this generation of Pokemon was featured.

While the anime has showcased different colorations of Pokemon prior to the concept of shiny Pokémon in the games, these variations are not officially recognized as shiny. The reasons behind these differences are often explained within the episodes, although this is not always the case.

In this episode of , Ash and his friends meet a trainer named Keenan, who owns a Sudowoodo that is entirely gold. This unique color results from a scientific experiment that made the Imitation Pokémon immune to Water-type attacks.

However, the gold Sudowoodo attracts too much unwanted attention, particularly from the troublesome Team Rocket. In response, Keenan promises to return his Pokémon to its original form. By the end of the episode, he fulfills that promise, removing the Sudowoodo's distinctive gold coloring and transforming it back into a regular Sudowoodo.

The Orange Islands arc introduced a variety of Pokémon with unique colorations, particularly those from Pinkan Island, which is known for its pink creatures. This distinctive color comes from their diet of Pinkan Berries. In one episode, Ash’s Pikachu even turns partially pink after eating one of these berries.

Several Pokémon, including Nidoking, Electabuzz, Geodude, and Mankey, are depicted as pink. These creative choices enhance the world of Pokémon, and the concept may also draw inspiration from real-life flamingos, which turn pink due to their diet.

The gang travels to Valencia Island during the Orange Islands arc, where they encounter several Pokemon that have slightly different coloration than usual. While these Pokemon have the same base colors, their tones are darker. This phenomenon led Professor Ivy to stay on the island to study them.

The Pokemon showcased include Butterfree, Raticate, Nidoran, Vileplume, Paras, and Weepinbell. It's a shame that fans did not see more of these unique Pokemon, and it would have been nice if one of the main characters had caught one to highlight this different style in future episodes of the anime. This was an example of regional variants, 17 years before they were officially announced in the franchise.

While Ash and Brock were training for the Pokemon League, they were interrupted by a giant Gengar and Alakazam, both of which had unique markings on their bodies. It was revealed that these Pokemon were considered gods in the ancient city of Pokemopolis.

The two Pokémon began to fight, but they were eventually calmed down by another giant Pokémon, a Jigglypuff, which used its song to soothe the two giants. Although this is a minor example of Pokémon with alternate colorings, it certainly enriches the lore of the series, suggesting that at one time in the universe, giant, god-like Pokémon roamed freely.

A lesser-known example is Puka, a Pikachu discovered in the Seafoam Islands alongside the trainer Victor. This Pikachu has striking blue eyes instead of the usual black and appears noticeably older, with wrinkles on its face.

Another interesting trait of this version of the franchise mascot is that it can surf, a characteristic that has been associated with Pikachu since the surfing Pikachu minigame in . Puka is also considered a significant inspiration for the design of Alolan Raichu, which shares its blue eyes and also surfs, albeit on its tail.

The history of the purple Kecleon is quite fascinating, as it has appeared in various forms of Pokemon media; however, it does not exist in the mainline games. Many fans mistakenly believe that the purple version is the shiny form, but in reality, shiny Kecleon is quite similar to the regular version, featuring a blue stripe instead of red.

The purple Kecleon first appeared in The Kecleon Caper, alongside the standard green variant, marking the introduction of the first Generation 3 Pokemon in Generation 2. It has also made appearances in the franchise and in the animated special based on the games. Despite its popularity, purple Kecleon is not an official Pokemon in the games.

In the second episode of the Pichu and Pikachu's Winter Vacation shorts from 2001, the gang's Pokemon encounter a group of Snorlax that have seemingly adapted to the colder climate. These Snorlax have a pale coloring and are depicted using the move Blizzard, suggesting they may have Ice-type characteristics.

This serves as an early example of regional variants in the Pokemon universe, similar to how Vulpix and Sandshrew adapted in Alola. It shows that Pokémon can adjust to colder environments. However, these Snowman Snorlax have only appeared in these shorts and have not been featured in any subsequent games or series.

During the events of the first Pokemon movie, , Mewtwo clones the Pokemon of those invited to New Island. Some of these cloned Pokemon have distinct markings that set them apart. Charizard, Venusaur, and Blastoise all look similar but feature colored markings on their skin, which may serve to differentiate them visually in the movie. This adds a unique and impressive aesthetic.

Another clone is Pikachu, referred to as Pikachutwo, which is nearly identical to the original Pikachu except for two small spikes on its ears. The cloned Pokemon make a few more appearances in the anime, particularly in the follow-up short .

A well-known example of an alternate-colored Pokemon is the Crystal Onix, which was discovered on Sunburst Island in the Orange Islands. This variant resembles a regular Onix but features a stunning crystal exterior that also grants it resistance to Water-type attacks, which is a significant weakness for regular Onix.

Unfortunately, the Crystal Onix is exclusive to the anime, despite many fans speculating that it might appear as a regional variant in . However, this did not come to pass, and many fans continue to be fascinated by this Pokémon, often featuring it in fan art and fan-made games.

One of the most famous examples of an alternate-color Pokémon in the anime is the Pink Butterfree, which became the mate of Ash's Butterfree. This moment led Ash to release his Butterfree, marking one of the saddest moments in anime history. This Butterfree was similar to the typical version, but instead of the usual purple body, it had a pink body.

The episode did not explain the reason for this color change, but there is a long-standing theory that this Butterfree comes from Pinkan Island in the Orange Islands. Notably, it is one of the few alternate-colored Pokémon to appear multiple times; it has shown up in various flashbacks, made an appearance alongside Ash again in the Journeys series, and was featured in the movie, which presents an alternate continuity.