The rare Pokémon in Pokémon Go also happen to be the creatures that sit on top of all the charts. These are the best Pokémon both for fighting at gyms and for protecting them from opposing players.
There are no clear-cut charts on Pokémon rarity in Pokémon Go. Early infographics on the subject did not agree with each other (see examples here and here), and developer Niantic has made plenty of changes to the game since its release in July 2016.
Rare Pokémon in Pokémon Go: Checking the Global Nest Atlas for clues
The best way to measure Pokémon rarity in Pokemon Go may be to use tools like the Global Nest Atlas, a worldwide map of Pokémon spawn points developed by fan community The Silph Road. By monitoring the results on the Global Nest Atlas and looking for Pokémon that are rarely being reported, you can get an idea as to which Pokémon are particularly rare in Pokémon Go.
But that information in and of itself may not be very helpful when it comes to figuring out which Pokémon you ought to be hunting. Just because a Pokemon is rare doesn't mean it's useful for gym battling. And if gym battling is your game, we know precisely which rare Pokémon you ought to be hunting.
Rare Pokémon in Pokémon Go: Snorlax and Lapras are the best.
If we are talking about Pokémon that spawn naturally in the world — in other words, excluding uncatchable Pokémon evolutions from the list — the two rarest and most combat-effective Pokémon in Pokémon Go must be Snorlax and Lapras.
You may wind up adding more Snorlax and Lapras into your Pokémon collections via hatching 10km eggs than by ever catching either of them in the wild. These Pokémon are so rare that even if you catch one, having enough candy to power up a Snorlax or Lapras might be extremely difficult. Candy is primarily obtained through catching and hatching Pokémon, but you can also earn it through the game's Buddy system.
Rare Pokémon in Pokémon Go: Dratini and Eevee lead to Dragonite and Vaporeon.
If we are focusing on capturing Pokemon that are powerful in Pokemon Go's gym battling endgame, then Dratini and Eevee should always be priority catches for any serious player. Not because they are particularly powerful, but because they evolve into tough fighters.
Dratini evolves into Dragonair and then into Dragonite, which happens to be one of the best gym attackers in Pokémon Go. However, Dratini are not always easy to find. So make sure you hunt down any that appear in the Nearby menu before attempting to catch anything else.
Based on personal experience, Eevee seems to be more common than Dratini, which is excellent because it has three evolutions. One of Eevee's evolved forms, Vaporeon, has been widely considered as a top-tier Pokémon in Pokémon Go ever since the game's launch. Vaporeon currently ranks high on top 10 and top 20 lists, especially on gym attacker rankings.
Eevee is especially attractive to hunt because you can control Eevee's evolution using a simple trick. If you rename the Eevee Rainer, Pyro or Sparky, then exit and reload Pokémon Go, you can evolve the renamed Eevee into a Vaporeon, Flareon or Jolteon respectively.
Or, to put it another way, it should be easy for you to repeatedly spawn a Vaporeon until you get one with the optimal moveset. That's a huge advantage for new trainers!
Rare Pokémon in Pokémon Go: The rarest ones are still missing.
Pokémon Go draws its roster of Pokémon from the "main" Pokémon games. Gen 1 Pokémon in Pokémon Go came from Pokémon Red and Blue, and the few Gen 2 Pokémon introduced so far originally hail from Pokémon Gold and Silver.
Mew, Mewtwo and the three Legendary Birds (Articuno, Zapdos and Moltres) are some of the most powerful Gen 1 Pokémon around. They're still missing from Pokémon Go, but they may be buried in the game's code awaiting release by Niantic. We don't know for sure, but early ads for Pokémon Go did feature Mewtwo in a giant battle in Times Square against hundreds of players.
We haven't had any massive flash mob Pokémon Go battle yet. However, if and when Mew, Mewtwo, Articuno, Zapdos and Moltres are released into the game, they will likely become the rarest and most-sought-after Pokémon in the game overnight.
More Pokémon Go news, tips, tricks and updates
If you have your sights set on the rarest Pokemon in Pokémon Go, you may also want to check out Mic's other Pokémon Go tips and tricks. Here are guides on how to catch Gen 2 baby Pokémon, the 98 Gen 2 Pokémon that have yet to be added to the game, how to catch Pikachu and his adorable new Christmas hat, our analysis of post-update Chansey and Rhydon, everything you need to know about finding the long-awaited Pokémon Ditto, how to create new PokéStops, how to maximize your chances of catching Pokémon and how PokéStops distribute Pokémon eggs.