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There are all the 3rd gen Pokémon in the two games, but like always there are some Pokémon that not appear on each game, and however this don´t affect the story line, this is a list of this Pokémon.

If you do have both games you can share your Pokémon to complete this list, but if you see a mission to rescue this Pokémon in his game (i.e. escort Feebas to Milotic in Red or Magikarp to Gyrados in Blue) then you can share the Wonder Mail code to the other game (register the code at the main menu) and do the mission (ie. complete Feebas mission in Blue or the Magikarp mission in Red). You will see the collected Pokémon in that game now. Later we´ll bring some Wonder Mail Codes to rescue all this Pokémon and see them in the dungeons (be aware of Gyrados; Milotic and the Plusle and Minum combo cause his abilities, Plus and Minus, and they are now more powerful).

[edit] Blue Version

Name	Type(s)	Area	Floor(s)	Size	% of Recluitment!
Magikarp	Water	Waterfall Pond	7-11	*
Gyrados	Water/Flying	Evolves from Magikarp at lv. 20		****
Lapras	Water/Ice	Far-off Sea	45-50	****
Aipom	Normal	Uproar Forest	1-6	*
Porygon 2	Normal	Buried Relic Wish Cave Joyous Tower Evolves from Porygon with an Upgrade and a Cable link	10-14, 16-18 79-84 80-84	*
Minium	Electric	Thunderwave Cave Lightning Field Joyous Tower Purity Forest	4-5 7-19 5-8 10-12	*

[edit] Red Version

Name	Type(s)	Area	Floor(s)	Size	% of Recluitment!
Feebas	Water	Waterfall Pond	16-19	*
Milotic	Water	Evolves from Feebas with Beauty Scarf		****
Mantine	Water/Flying	Grand Sea	30	**
Roselia	Grass	Uproar Forest	4-7	*
Porygon	Normal	Buried Relic	5-10	*
Plusle	Electric	Thunderwave Cave Lightning Field Joyous Tower Purity Forest	4-5 7-19 5-8 10-12	*