PokéBase - Pokémon Q&A
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It needs to be near Lilycove, because that's where I am right now.

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Which game, Emerald, Ruby/Sapphire, or OR/AS?
Swellow
Swellow or Flygon if you also want to use it in battle, Tropius if you just want a convenient HM slave.
CROBAT

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Without Surf: Go west of Lilycove to Route 121, and a L26-28 Wingull can be found in the grass with a 9% Spawn rate.

With Surf: Surfing within Lilycove itself yields a L10-30 Wingull with a 35% spawn rate, and L25-30 Pelipper with a 5% Spawn rate (which are technically 'the nearest Pokemon that can Fly' if your starting point is Lilycove).

Alternatively, in the Safari Zone, if you don’t want Wingull/Pelipper:

  • L25 Doduo or L25 Natu (which requires 1 level up to evolve into Xatu, which can learn Fly) can be found in the first Safari Zone area, each with a 10% spawn rate.
  • L27-29 Doduo can be found in the 3rd Safari area with a 15% spawn rate.
  • L27-29 Dodrio can be found in the 3rd Safari area with a 5% spawn rate.
  • L27-29 Natu can be found in the 4th Safari area with a 15% spawn rate (requires 1 level to evolve and learn Fly).
  • L29-31 Xatu can be found in the 4th Safari area with a 5% spawn rate.
  • L35 Hoothoot can be found in the 5th and 6th Safari areas with a 5% spawn rate.

Personal recommendation:

If you just want a Fly HM slave: go with a Wingull.

If you’re after something with a bit more grunt: Doduo/Dodrio is fast + packs a punch, and is probably better than the other options as you already have 4 special attacking Pokémon on the team (well, 2 mixed in Blazekin/Marshstomp and 2 Special in Grovyle/Kirlia). Plus Dodrio wrecks Ghosts, though in Emerald, 2 of 5 of Phoebe’s Pokémon carry coverage moves against birds, so it pays to be careful (1 Banette has T-Bolt and reasonable Special Attack, 1 Dusclops has Rock Slide and reasonable Physical Attack).

If you end up going with Doduo: I would recommend withholding its evolution (ie mash B on evolution screen) until level 37, so that it can learn Drill Peck earlier (instead of waiting until level 47 as Dodrio).

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this doesn't answer the question.
The asker is asking which pokemon will fit his team well that can learn fly.You are giving only suggetion without discussing which will suit his requirement the best.
@loki ron

“I need the nearest Pokémon that can learn Fly.” (Pokémon Emerald)

(Mentions 2 Wingull locations, with and without Surf, that both qualify as ‘the nearest Pokémon that can learn Fly’).

(Provides multiple ‘nearby’ alternatives in case they don’t want Wingull)

Did the OP ask which one would suit their requirement best? Other than ‘nearest’? If so, it’s Wingull.

I guess I’ll add a personal recommendation too. And a bunch of other information and justifications for things.

You guys are a tough crowd here, lol.
Why is Wingull better than Tropius?
For a throwaway HM slave? Wingull is a lot closer.  From Lilycove, Tropius requires backtracking through R120 > Fortree City > R119. Wingull meanwhile is 'nearer' in R120 or within Lilycove itself, and the OP's original statement was:

"I need the NEAREST Pokemon that can learn fly".

In the event that the OP wasn't after a throwaway HM slave however, alternatives in the Safari Zone (which is also quite close) were suggested (I'd recommend Doduo as it brings some physical damage to a team of mostly Special attackers). As for Tropius as a serious Pokemon: Wouldn't that mean doubling up on Special Attacking Grass types?