Feebas may be the hardest Pokémon to find, but Milotic is not the rarest (like many people believe). Here’s why:

To catch Feebas, you must canvas an entire river on only a single route to find one of five possible tiles Feebas will appear on.
You must fish in each tile multiple times because other pokemon may appear on Feebas’ tile, giving you false negatives. If after 5-6 encounters there is still no Feebas, it means Feebas is very unlikely to be there, so move on to the next tile. Repeat this until you find a Feebas.
If your luck truly is terrible enough, and you have searched the entire river without hide nor hair of Feebas, you have to do it all over again.
There exist people who have found Feebas tiles but reading their story or watching their video won’t help you. Do not go to the same tile they went to expecting to find a Feebas, because your tiles are totally random and won’t be like any other game cartridge.
If you feel like shuffling the tiles will help you find Feebas, go to Dewford and change the “Trendy Phrase.” It doesn’t matter what you change it to and you can find Feebas without ever setting a trendy phrase. Feebas tiles will stay the same throughout the entire game unless you manually shuffle them.
Once you find Feebas, you can catch as many as you want, which means they are not rare at all, just really hard to find.
To get a Milotic, raise Feebas’ beauty to max. Raise its level by one (I recommend a Rare Candy to speed up this exciting process) and it’ll evolve into Milotic.

So you can actually get hundreds of Milotic if you want. Not to mention, the only HM you need is Surf so you can go for Feebas before you even battle your rival on your way to Fortree City. You’ll see the occasional trainer who has a Milotic, which is why I say Milotic is not the rarest, merely hard to find.

The actual rarest Pokémon is held by one trainer in the entire game—Drake of the Elite Four. The last and strongest of the toughest trainers in all of Hoenn. Second only to the Champion himself.

Salamence.

You can find Bagon back in Meteor Falls but only in late-game, as you need Waterfall and Surf to reach him. So after backtracking to Meteor Falls, you have to go to the absolute deepest prt of the cave until you can’t go any farther, nowhere else to go. Surf to the back and on this tiny patch of land, run around until you find Bagon. He has a 20% encounter rate so it‘ll probably take a few battles before you find one. Catch him, smile at this accomplishment, and then watch your spirits dampen as you realize the grind time you’re about to put in. You HAVE to be determined to get Salamence because by the time you can reach Bagon, he is extremely underleveled compared to the rest of your team. And Shelgon evolves at level 55, while being a terrible Pokémon to battle with until he becomes the incredible Salamence you’ve been dying for. This grind will hurt you. It’s just about as agonizing as obtaining a Milotic. But if you do get Salamence, you’ll officially have the rarest Pokémon in the entire game—excluding the legendaries, those are obvious.

Other rare Pokémon include Aggron, Metagross, Ludicolo, Altaria, and Slaking.

I am only including Pokémon that are not obtained by trading which is why some of them are not listed (Golem, Alakazam, etc.).

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