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This here is a very, very simple list of every Pokemon seen and captured in the main comic. It does not apply to Battle Frontier.

#001 - Bulbasaur (Red/Erika)

#002 - Ivysaur (Red/Erika)

#003 - Venusaur (Red/Erika)

#004 - Charmander (Gary/Red)

#005 - Charmeleon (Gary/Red)

#006 - Charizard (Gary)

#007 - Squirtle (Green/Red)

#008 - Wartortle (Green)

#009 - Blastoise (Seen)

#010 - Caterpie (James)

#011 - Metapod (James)

#012 - Butterfree (James)

#013 - Weedle (James)

#014 - Kakuna (James)

#015 - Beedrill (James)

#016 - Pidgey (Gary)

#017 - Pidgeotto (Gary)

#018 - Pidgeot (Gary)

#019 - Rattata (Gary)

#020 - ???

#021 - Spearow (Seen)

#022 - ???

#023 - Ekans (Gary)

#024 - Arbok (Gary)

#025 - Pikachu (Green/Red/Surge)

#026 - Raichu (Surge)

#027 - Sandshrew (Gary)

#028 - ???

#029 - Nidoran F (Green)

#030 - Nidorina (Green)

#031 - Nidoqueen (Green)

#032 - ???

#033 - Nidorino (Seen)

#034 - ???

#035 - Clefairy (Green)

#036 - ???

#037 - Vulpix (Red)

#038 - Ninetales (Red)

#039 - Jigglypuff (Green)

#040 - ???

#041 - Zubat (Brock)

#042 - ???

#043 - Oddish (Erika)

#044 - Gloom (Erika)

#045 - Vileplume (Erika)

#046 - Paras (James)

#047 - ???

#048 - Venonat (Sabrina)

#049 - Venomoth (Sabrina)

#050 - Diglett (James)

#051 - Dugtrio (James)

#052 - Meowth (Seen)

#053 - ???

#054 - Psyduck (Misty)

#055 - Golduck (Misty)

#056 - Mankey (Gary)

#057 - Primeape (Gary)

#058 - Growlithe (Seen)

#059 - Arcanine (Seen)

#060 - ???

#061 - ???

#062 - ???

#063 - Abra (Sabrina)

#064 - Kadabra (Sabrina)

#065 - Alakazam (Sabrina)

#066 - Machop (Seen)

#067 - Machoke (Gary)

#068 - Machamp (Gary)

#069 - Bellsprout (Erika)

#070 - Weepinbell (Erika)

#071 - Victreebel (Erika)

#072 - ???

#073 - ???

#074 - Geodude (Brock)

#075 - Graveler (Brock)

#076 - ???

#077 - ???

#078 - ???

#079 - ???

#080 - ???

#081 - Magnemite (Surge)

#082 - ???

#083 - ???

#084 - ???

#085 - ???

#086 - ???

#087 - ???

#088 - ???

#089 - ???

#090 - Shellder (Seen)

#091 - ???

#092 - Gastly (Sabrina)

#093 - Haunter (Sabrina)

#094 - Gengar (Sabrina)

#095 - Onix (Brock)

#096 - ???

#097 - ???

#098 - Krabby (Seen)

#099 - ???

#100 - Voltorb (Surge)

#101 - Electrode (Surge)

#102 - Exeggcute (Erika)

#103 - Exeggutor (Erika)

#104 - ???

#105 - ???

#106 - Hitmonlee (Seen)

#107 - Hitmonchan (Seen)

#108 - Lickitung (Seen)

#109 - ???

#110 - ???

#111 - Rhyhorn (Gary)

#112 - ???

#113 - ???

#114 - Tangela (Erika)

#115 - Kangaskhan (Seen)

#116 - Horsea (Misty)

#117 - Seadra (Misty)

#118 - Goldeen (Misty)

#119 - ???

#120 - Staryu (Gary/Misty)

#121 - Starmie (Misty)

#122 - Mr. Mime (Sabrina)

#123 - Scyther (James)

#124 - ???

#125 - ???

#126 - ???

#127 - ???

#128 - ???

#129 - ???

#130 - Gyarados (Misty)

#131 - ???

#132 - Ditto (Green)

#133 - Eevee (Red/Surge)

#134 - ???

#135 - Jolteon (Surge)

#136 - ???

#137 - ???

#138 - Omantye (Gary)

#139 - ???

#140 - Kabuto (Brock)

#141 - Kabutops (Brock)

#142 - Aerodactyl (Brock)

#143 - ???

#144 - Articuno (Seen)

#145 - Zapdos (Red)

#146 - ???

#147 - ???

#148 - ???

#149 - Dragonite (Seen)

#150 - Mewtwo (Seen)

Other Pokemon:

#??? - Pichu (Seen)

#??? - Smoochum (Seen)

#??? - Houndoom (Seen)

Logged Pokedexes:

Gary - Green - Red - James - Brock - Sabrina - Misty - Erika - Lt. Surge

History:

The Pokedex started out as a book written by young Samuel Oak of Kanto. He recorded every single Pokemon he saw, which included some new ones. He named this book 'Pokedex 1.' However, the book only contained names. He went back and learned about all these Pokemon, and eventually made a 'Pokedex 2' book, which was sold as a guide to all young trainers for a small price. Pokedex 2 contained actual information on the creatures. He would continue researching Pokemon for many years, and eventually, a new idea for the Pokedex was made. It was to be an electronic handheld device that could be carried around much better than Oak's large book. These electronic Pokedexes (Handheld Pokedex V1) were given to the Gym Leaders and Oak. Every three years or so, the Pokedex is updated with all the native Pokemon.
There are different Pokedexes for different parts of the nation. For example, Hoenn's Pokedex doesn't include Bulbasaur because you can't find it there, either in nature or the Safari Zone. Kanto's Pokedex logically doesn't include Mudkip, because it is found in Hoenn.