Canon

Canon refers to all official and undeniable information within a general series. Originally a religious term used to refer to which scriptures written "counted" in a religion, the term has expanded to have meaning in fictional continuities as well.

In the Pokémon franchise there are several canons, usually sharing elements and concepts among them, most notably the existence of Pokémon. Aside from this and the interrelation of the various species of Pokémon (such as by evolution), these worlds can vary from one another in canon and storyline either very little or very greatly.

Canon is different from fanon in that, while fanon things may be mutually agreed upon by most, and possibly all, fans, they are never officially stated.

List of canons

Games

The canon of the core series considers the following:

Events occurring in the core series games are the ultimate canon.
Player choices such as the hero's gender and starter Pokémon are generally not standardized within the canon, with the exception of Red in the Generation I games and their remakes, who possesses all three starters (four if counting Pikachu) in later games.
In the case of conflicts between versions of a game, the later one such as a third version or remake, supersedes. As such, Pokémon Crystal Version canonically supersedes its paired counterparts Pokémon Gold and Silver Versions, and is itself superseded by remakes Pokémon HeartGold and SoulSilver Versions. If equally new versions, such as paired versions, conflict, the canonical one is generally not standardized.
Content from games related to the core series is canon unless it conflicts with events in the core series games, while content from unrelated spin-offs is generally non-canon.
Canonical material via other forms of media, like animated trailers, manuals or merchandise, may exist depending on each case.

Anime

The canon of the Pokémon anime considers the following:

The events of each and every episode are canon, and occur in chronological order with the exception of EP052 and EP053, which takes place before EP049. Also, the special episodes Holiday Hi-Jynx and Snow Way Out! take place either directly before or after EP039 (airing of these and some other episodes was postponed due to EP038 incident).
All movies except Pokémon the Movie: I Choose You! are canon to the TV series (although only one of the two versions of the 14th movie is canon), and usually act the same as filler episodes, as Ash and his friends do not obtain, evolve, or release any Pokémon, and do not earn any Badges or Ribbons. Often a movie takes place chronologically between the episodes which it premieres between in Japan.
The Japanese version of the anime supersedes any and all dubs if there is conflict between them, unless the dub corrects an obvious error. If something is said in a dub that is not mentioned in the original, it may or may not be canon.
Pokémon Origins and Pokémon Generations are separate series from the Pokémon anime, so are separate canons.

Manga

The canon of the various Pokémon manga considers the following:

Each manga series is a separate canon, except in instances of sequels, such as Pokémon Chamo-Chamo ☆ Pretty ♪, which follows from Magical Pokémon Journey.
Pokémon Adventures chapters and rounds follow chronologically from one another, rather than having the Ruby & Sapphire and Emerald arcs occur contemporaneously to the Red, Green & Blue and Yellow arcs as the storylines of the games they are based on do. The same applies to Diamond & Pearl and Platinum arcs which do not occur simultaneously with the Gold, Silver & Crystal arc. The exceptions to this rule are the HeartGold & SoulSilver and Omega Ruby & Alpha Sapphire arcs, both of which occur between Emerald and Diamond & Pearl. Although the rounds of a chapter follow chronologically from one another there are few exceptions to this: for example, Buzz Off, Butterfree! (round 152) takes place simultaneously with Slugging It Out With Slugma (round 117).
- W Mission Story: Pokémon Ranger - the Comic and Darkrai Mission Story: Pokémon Ranger Vatonage - the Comic, although not strictly related, are considered to be canon within Pokémon Adventures, as evidenced in The Final Dimensional Duel XI.

Differences between canons

Characters that are well known in the Pokémon franchise can have vast differences between the various canons. For example, in the games, Brock is a well-known Gym Leader, the toughest Trainer in the area of Pewter City, and remains as the leader of its Gym between the time of Red/Leaf's journey and Ethan/Kris/Lyra's. In the anime, however, while he is a tough Trainer, his true calling is as a Pokémon Breeder (and later on, a Pokémon Doctor), and he took the mantle of Pewter Gym Leader only because both of his parents left on their own Pokémon journeys, leaving him in the care of the Gym and their rather large family. Differences can go much further than that, with Sabrina being a kind shrine maiden in The Electric Tale of Pikachu, a misguided young woman due to the development of her powers in the anime, and a Team Rocket member in Pokémon Adventures.