Forum Thread

When having shadow pokemon in boxes with regular and shiny pokemon, the order isn't always the same. My Caterpie line goes Caterpie (Normal), Caterpie (Shiny), Caterpie (Shadow) - but Metapod goes Metapod (Shadow), Metapod (Normal), Metapod (Shiny). My three Butterfree line up with the Caterpie, but when I look at my two Raichu, they're listed as Raichu (Shadow) and then Raichu (Normal), so I'm not sure which order they're really supposed to be in.

I assume pokemon order is supposed to be normal, shadow, shiny.
image link (sorry, low quality).

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I believe it actually is in order of dex number, then ID (time obtained). Since Shinies/Shadows are actually counted as the same dex number / species as the normal form, they would be ordered by ID, not the shiny/shadow-ness.

As Lycario said, the way your pokemon are ordered in your boxes is determined by 2 factors: their pokedex number and their pokemon ID (unique number given when you adopt a new egg).
Normalness, shinyness and shadowness doesn't affect to the display order in your boxes because they are related to the sprites not to the dex number.

In other words, for the same pokedex number, you can have up to 3 kind of different sprites (well, some more if we count gender differences, but that's another story). Those 3 kind of sprites are also determined by a number, "zero" for normal sprites, "one" for shiny sprites and "two" for shadow sprites. That secondary number doesn't affect the way your pokemon are ordered.

To give an example (you can see the difference in the url of the links below), Ampharos, whose dex number is #181, can have 3 kind of sprites but they all will have the same dex number:

The sprite number for Normal ampharos would be 0181
The sprite number for Shiny ampharos would be 1181
The sprite number for Shadow ampharos would be 2181

For the box order, all this 3 pokemon are considered the same, and the way they'll be ordered will be determined by their ID

ADDITIONAL INFO:

Though this is not exactly in your question something that is also related to it is the way how events, gigas and megas are ordered in your boxes.

You might think they are also disordered, but they follow the same rule said above. First of all they'll be ordered by their dex number but this time followed by letters and then by their pokemon ID.
All those events/megas/gigas will be displayed in alphabetical order depending on those letters.

Again, I'll use ampharos as example, as it has plenty of events and megas. This is the order they will be displayed in boxes:

#181 Ampharos whose dex number is 181
#181 Mega Autumn Ampharos whose dex number is 181am
#181 Autumn Ampharos whose dex number is 181au
#181 Mega Ampharos whose dex number is 181m
#181 Mega Winter Ampharos whose dex number is 181mw
#181 Mega Summer Ampharos whose dex number is 181pm
#181 Spring Ampharos whose dex number is 181s
#181 Mega Spring Ampharos whose dex number is 181sm
#181 Summer Ampharos whose dex number is 181su
#181 Winter Ampharos whose dex number is 181w