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The canon is all official (and thus undeniable) information within the Pokémon franchise. This includes characters, locations, events, and all aspects of the Pokémon universe.

As opposed to other works of fiction, Pokémon canon does not always overlap within the different works. Each universe has its own depiction of the Pokémon world.

As such, there are several different works with individual canons:

This generally includes only Pokémon RPGs created directly by GameFreak. The others still apply, but are overridden by the aforementioned games.
This combines the original series, Advanced Generation, Diamond and Pearl, and generally the movies and all OVAs. The movies are sometimes considered to be out of continuity with the series, but there have been cross-overs, such as Ash remembering Lugia from the second movie. There is contention between those who believe the English dub is non-canon and those who do.
Each manga is a completely seperate entity from the rest. Pokémon Special is not in the same universe as the Electric Tale of Pikachu, nor is it in the same universe as Pokémon Zensho, and so on.
Trading Card Game
Although there is too little information to consider the Trading Card Game as having a complete canon in and of itself, some aspects of the Trading Card Game do not appear in other contexts.

The canons can differ to different degrees. For example, the Gym Leader Misty has similar basis but each work gives her a different spin; in the anime, she is very caring and supportive but can be mean at times; she is powerful and flirtatious in the Electric Tale of Pikachu manga; and in the games, she is considered a tomboy. Although it isn't to say that none of these attributes can coexist, it would be difficult to simplify all the different interpretations into a single, unified mythology.

Within different contexts, one work can influence another. Generally, the starting point for all characters begins with the games and the original Sugimori game art. For this reason, the games can take precedence when there is a conflict within a single work, or when there is nothing said about a certain topic within the work. Similarly, the Electric Tale of Pikachu manga is very loosely based on the anime, which is in turn loosely based on the games.

In nearly all cases, the original Japanese version of any particular work is canon over any foreign-language translation (including English). Furthermore, any work that is not based in Japan (and thus not under the general direction of Satoshi Tajiri) is generally considered non-canon (Pokémon Live!, for example).

Some aspects are present in all works, but usually only when the scope is very broad. For example, the notion that people called Pokémon trainers battle creatures called Pokémon is canon in all works. Canon diverges slightly into different universes when one must specify the ultimate goal for trainers (generally a Pokémon Master, but its definition is open to interpretation within different contexts). Canon may diverge further when it comes to increasingly specific details, such as how exactly a trainer utilizes a Poké Ball or TM.

According to Tajiri, the Pokémon Special manga is the closest to the world he was trying to convey.

Almost all kinds of shipping are considered fanon - i.e non-canon.