The little holes you can see on walls in Pokémon Emerald are portals to secret bases. Buy a TM (Technical Move) named Secret Power and teach it to one of your Pokémon in your party. Go to any holes and it will dig up. Inside where spacious area where you can put your stuffs there, ready for decorations and customization.
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they are secret bases you need to teach a Pokemon secret power first to use them
The dark spots in water are not holes. They are little ways to tell you there is a rarer Pokemon there. It's the water equivalent of shaking grass.
If you mean all the Pokemon in the entire game, that's a little hard to answer. Be more specific.
its not an emerald its RAYQUAZA the main legendary Pokemon in Pokemon emerald.
I think you should learn your pokemon strength and use it against the holes. I just think that,because alot of people say that.