Here is the new numbering system seen in Ruby/Sapphire. It is completely over-hauled and 100% confirmed. So you guys best start learning the new numbers. This is for the Pokémon that are obtainable in R/S:

New. No. Old. No. Picture Jp. Name US. Name
#001 #252
Kimori Treecko
#002 #253
Jupotol Grovyle
#003 #254
Jukain Sceptile
#004 #255
Achamo Torchic
#005 #256
Wakashamo Combusken
#006 #257
Bashamo (Bursyamo) Blaziken
#007 #258
Mizugorou Mudkip
#008 #259
Numakorou Marshtomp
#009 #260
Rugaji Swampert
#010 #261
Pochena Poochyena
#011 #262
Guraena Mightyena
#012 #263
Jiguzaguma Zigzagoon
#013 #264
Massuguma Linoone
#014 #265
Kemusso Wurmple
#015 #266
Karasairu Silcoon
#016 #267
Agehanto Beautifly
#017 #268
Mayurudo Cascoon
#018 #269
Dokukeiru Dustox
#019 #270
Hasuboo Lotad
#020 #271
Hasubrero Lombre
#021 #272
Runpapa Ludicolo
#022 #273
Taneboo Seedot
#023 #274
Conohana Nuzleaf
#024 #275
Daatengu Shiftry
#025 #276
Subame Taillow
#026 #277
Oosubame Swellow
#027 #278
Kyamome Wingull
#028 #279
Perippa Pelipper
#029 #280
Rarutosu Ralts
#030 #281
Kiruria Kirlia
#031 #282
Saanaito Gardevoir
#032 #283
Ametama Surskit
#033 #284
Amemoosu Masquerain
#034 #285
Kinokoko Shroomish
#035 #286
Kinogassa Breloom
#036 #287
Namakero Slakoth
#037 #288
Yarukimono Vigoroth
#038 #289
Kekkingu Slaking
#039 #063
Kesie Abra
#040 #064
Yungera Kadabra
#041 #065
Fudin Alakazam
#042 #290
Tsuchinin Nincada
#043 #291
Tekkanin Ninjask
#044 #292
Nukenin Shedinja
#045 #293
Gonyonyo Whismur
#046 #294
Dogoomu Loudred
#047 #295
Bakuong Exploud
#048 #296
Makunoshita Makuhita
#049 #297
Harieteyama Hariyama
#050 #118
Tosakinto Goldeen
#051 #119
Azumao Seaking
#052 #129
Koiking Magikarp
#053 #130
Gayaradosu Gyarados
#054 #298
Ruriri Azurill
#055 #183
Mariru Marill
#056 #184
Mariruri Azumarill
#057 #074
Ishitsubute Geodude
#058 #075
Gouron Graveler
#059 #076
Gouronya Golem
#060 #299
Nozupasu Nosepass
#061 #300
Eneko Skitty
#062 #301
Enekororo Delcatty
#063 #041
Zubatto Zubat
#064 #042
Gorubatto Golbat
#065 #169
Kurobatto Crobat
#066 #072
Menokurage Tentacool
#067 #073
Menokurage Tentacruel
#068 #302
Yamirami Sableye
#069 #303
Kuchiito Mawile
#070 #304
Kokodora Aron
#071 #305
Kodora Lairon
#072 #306
Bossugodora Aggron
#073 #066
Wanriki Machop
#074 #067
Gorikii Machoke
#075 #068
Kairikii Machamp
#076 #307
Asanan Meditite
#077 #308
Chaaremu Medicham
#078 #309
Rakurai Electrike
#079 #310
Raibolt Manectric
#080 #311
Purasuru Plusle
#081 #312
Mainan Minun
#082 #081
Koiru Magnemite
#083 #082
Reakoiruu Magneton
#084 #100
Biriridama Voltorb
#085 #101
Marumain Electrode
#086 #313
Barubitto Volbeat
#087 #314
Irumiize Illumise
#088 #043
Nazunokusa Oddish
#089 #044
Kusaihana Gloom
#090 #045
Rafureissa Vileplume
#091 #182
Kiereihana Bellossom
#092 #084
Douduo Doduo
#093 #085
Doudariou Dodrio
#094 #315
Rozeria Roselia
#095 #316
Gokurin Gulpin
#096 #317
Marunoomu Swalot
#097 #318
Kibania Carvanha
#098 #319
Samehadda Sharpedo
#099 #320
Hoeruko Wailmer
#100 #321
Hoeruo Wailord
#101 #322
Donmeru Numel
#102 #323
Bakuuda Camurupt
#103 #218
Magumagu Slugma
#104 #219
Magukarugo Magcargo
#105 #324
Kootasu Torkoal
#106 #088
Betobeta Grimer
#107 #089
Betobeton Muk
#108 #109
Dogassu Koffing
#109 #110
Matadogassu Weezing
#110 #325
Banebu Spoink
#111 #326
Bupiggu Grumpig
#112 #027
Sandoo Sandshrew
#113 #028
Sandopan Sandslash
#114 #327
Paachiru Spinda
#115 #227
Eaamundo Skarmory
#116 #328
Nakkura Trapinch
#117 #329
Birubbaa Vibrava
#118 #330
Furaigon Flygon
#119 #331
Sabonea Cacnea
#120 #332
Nokutasu Cacturne
#121 #333
Chirutto Swablu
#122 #334
Chirutarisu Altaria
#123 #335
Zanguusu Zangoose
#124 #336
Habuneeku Seviper
#125 #337
Runatoon Lunatone
#126 #338
Sorurokku Solrock
#127 #339
Dojotchi Barboach
#128 #340
Namazun Whiscash
#129 #341
Heigani Corphish
#130 #342
Shizarigar Crawdaunt
#131 #343
Yajiron Baltoy
#132 #344
Nendooru Claydol
#133 #345
Ririira Lileep
#134 #346
Yureidoru Cradily
#135 #347
Anopusu Anorith
#136 #348
Aamarudo Armaldo
#137 #174
Pupurin Igglybuff
#138 #039
Purin Jigglypuff
#139 #040
Pukurin Wigglytuff
#140 #349
Hinbasu Feebas
#141 #350
Mirokarosu Milotic
#142 #351

Powarun Castform
#143 #120
Hitodemon Staryu
#144 #121
Starmie Starmie
#145 #352
Kakureon Kecleon
#146 #353
Kagebouzou Shuppet
#147 #354
Jupetta Banette
#148 #355
Yomawaru Duskull
#149 #356
Samayowa Dusclops
#150 #357
Toropiusu Tropius
#151 #358
Chiriin Chimecho
#152 #359
Abusoru Absol
#153 #037
Rokon Vulpix
#154 #038
Kyuukon Ninetales
#155 #172
Pichuu Pichu
#156 #025
Pikachuu Pikachu
#157 #026
Raichuu Raichu
#158 #054
Kodakku Psyduck
#159 #055
Gurudukku Golduck
#160 #360
Soonano Wynaut
#161 #202
Soonansu Wobbuffet
#162 #177
Neitei Natu
#163 #178
Neiteio Xatu
#164 #203
Kirinriki Girafarig
#165 #231
Gomazu Phanpy
#166 #232
Donfan Donphan
#167 #127
Kairosu Pinsir
#168 #214
Herakurosu Heracross
#169 #111
Saihorn Rhyhorn
#170 #112
Saidon Rhydon
#171 #361
Yukiwarashi Snorunt
#172 #362
Oonigori Glalie
#173 #363
Tamazarashi Spheal
#174 #364
Todogura Seoleo
#175 #365
Todozeruga Walrein
#176 #366
Paaruru Clamperl
#177 #367
Hanteeru Huntail
#178 #368
Sakurabisu Gorebyss
#179 #369
Jiiransu Relicanth
#180 #222
Saanigo Corsola
#181 #170
Chonchii Chinchou
#182 #171
Rantan Lanturn
#183 #370
Rabukasu Luvdisc
#184 #116
Tattsu Horsea
#185 #117
Shiidora Seadra
#186 #230
Kingudora Kingdra
#187 #371
Tatsubei Bagon
#188 #372
Kommoru Shellgon
#189 #373
Boomanda Salamence
#190 #374
Danbaru Beldum
#191 #375
Metangu Metang
#192 #376
Metagorosu Metagross
#193 #377
Rejirokku Regirock
#194 #378
Rejiaisu Regice
#195 #379
Rejisuchiru Registeel
#196 #380
Ratiasu Latias
#197 #381
Ratiosu Latios
#198 #382
Kaiorga Kyogre
#199 #383
Guraadon Groudon
#200 #384
Rekkuza Rayquaza
#201 #385
Jiraachi Jirachi
#202 #386
Deokishisu Deoxys

Pokémon Programmed in, but un-obtainable

 
All Content is ©Copyright of Serebii.net 1999-2014.
Pokémon And All Respective Names are Trademark & © of Nintendo 1996-2014