Before I start, I am going to say that because dragons are not real life creatures, I will not count them as reptiles, even though some of them are similar. I will count some like Dragonair that are based on snakes/serpents. I will also not count Pokemon that are obviously dinosaurs.
Bulbasaur line: frogs/toads
Charmander line: salamanders
Squirtle line: turtles
Ekans line: snakes
Poliwag line: tadpoles/frogs
Dratini/Dragonair: snakes
Totodile line: crocodiles
Wooper: axolotl
Quagsire: Salamander
Dunsparce: snake
Treecko line: geckos
Mudkip line: axolotl
Torkoal: tortoise
Seviper: snake
Milotic: snake
Kecleon: chameleon
Turtwig line: tortoise
Croagunk line: frogs
Heatran: frog
Snivy line: snakes
Tympole line: tadpoles/frogs
Sandile line: crocodiles
Tirtouga line: turtles
Froakie line: frogs
Helioptile line: lizards
Zygarde: snake
Salandit line: lizards
Turtonator: tortoise
Sobble line: lizards
Chewtle line: turtles
Silicobra line: snakes
Toxel line: lizards
Dreepy line: Diplocaulus/lizards
Fuecoco line: Crocodiles
Tadbulb line: Tadpoles/Frogs
Cyclizar: lizard
Clodsire: salamander?
Source
That's it! I went pretty vague as I was just skimming through the list of Pokemon, if you want more detail for specifics I'd be happy to give them.
If you think I missed any, please let me know!
