So, you’re looking at the 3DS eShop—or maybe digging through a bin of used cartridges—and you’re stuck. It’s the classic Pokémon dilemma. Do you go with the giant red dinosaur or the glowing blue whale? Honestly, picking between Omega Ruby Alpha Sapphire version exclusives isn't just about which legendary looks cooler on the box art. It changes your entire playthrough. It dictates your team composition, how you interact with the Hoenn region's villains, and even how you traverse the post-game Delta Episode.
Back in 2014, Game Freak didn't just give us a shiny coat of paint on the Gen 3 originals. They fundamentally tweaked the encounter tables. If you’re a completionist, you’re going to need a friend or a second console because some of these gaps are huge.
The Big Ones: Groudon vs. Kyogre
It starts with the mascots. Obviously.
If you pick Omega Ruby, you get Groudon. In this remake, it gets the Primal Reversion treatment, turning into a Fire/Ground type that basically deletes its 4x water weakness by evaporating the rain. It’s a beast. In Alpha Sapphire, you’re looking at Primal Kyogre. It stays a pure Water type but its Primordial Sea ability makes it an absolute nuke in the rain.
But it’s not just the legendary on the cover. The entire narrative flips. In Omega Ruby, you're fighting Team Magma. Maxie and his crew want to expand the landmass. They wear red, they use fire types, and they generally act like uptight scientists. If you go with Alpha Sapphire, you’re up against Team Aqua. Archie is basically a pirate, his base is full of water puzzles, and his motivation is flooding the world to save Pokémon habitats.
The "flavor" of your game is dictated by this choice.
Wild Pokémon You’ll Only Find in One Version
You’re walking through the tall grass on Route 102. If you have Omega Ruby, you’re going to run into Seedot. It eventually evolves into Shiftry, a weird Grass/Dark type that looks like a tengu. If you’re on Alpha Sapphire, that slot is taken by Lotad. Ludicolo is a fan favorite for a reason—it’s a Water/Grass type that dances its way through the elite four.
Here is the breakdown of the standard wild encounters you need to worry about.
In Omega Ruby, you have access to:
Mawile, which is a massive deal because its Mega Evolution was arguably the strongest thing in the game back in the day. You also get Zangoose, Solrock, and the aforementioned Seedot line. Later on, you can find Sawk in the wild.
In Alpha Sapphire, you’re getting:
Sableye, the cheeky little gem-eater that serves as the counterpart to Mawile. You get Seviper instead of Zangoose, Lunatone instead of Solrock, and the Lotad line. Instead of Sawk, you’ll find Throh.
It feels balanced on paper. But in practice? Mawile makes Omega Ruby a very tempting choice for competitive players who want to build a powerhouse Mega without trading.
The Legendary Problem: Mirage Spots
This is where things get complicated. Once you get the Eon Flute and start Soaring through the sky, you’ll see red sparkles over the map. These are Mirage Spots.
Game Freak used these remakes to dump almost every previous legendary into the Hoenn region. But they split them right down the middle. It’s frustrating if you’re trying to finish a National Dex alone.
Omega Ruby Exclusives:
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- Ho-Oh: You’ll find it on Sea Mauville after getting the Scanner.
- Palkia: You need both Uxie, Mesprit, and Azelf in your party to trigger this.
- Reshiram: Found in the Fabled Cave.
- Tornadus: You’ll find this in the clouds while Soaring.
Alpha Sapphire Exclusives:
- Lugia: Also at Sea Mauville, but it replaces Ho-Oh.
- Dialga: The counterpart to Palkia.
- Zekrom: The counterpart to Reshiram.
- Thundurus: Found in the sky.
There is a catch, though. To get the "third" legendary of these trios—specifically Landorus, Giratina, and Kyurem—you actually need both of the version exclusives in your party at the same time. This means if you have Omega Ruby, you can’t catch Giratina unless you trade for a Dialga from someone with Alpha Sapphire. It’s a clever, albeit annoying, way to force player interaction.
The Latios and Latias Factor
Midway through the game, Steven Stone takes you to Southern Island. This is a scripted event where a legendary joins your team for free. It’s one of the few times a high-tier legendary just hands itself to you without a fight.
In Omega Ruby, you get Latios. He’s the blue one, he’s faster, and he hits harder on the special side.
In Alpha Sapphire, you get Latias. She’s the red one, and she’s much bulkier.
Both can Mega Evolve, and both are used for the Soar mechanic. Interestingly, you can actually get the "other" one later if you have the Eon Ticket. Back in 2014, this was a StreetPass event. Today? You’ll likely need to use a save editor or find someone who still has the event flag on an old 3DS if you want to do it "legit." Otherwise, they are hard-locked exclusives.
Fossil Pokémon and Mega Stones
Don't forget the fossils. When you’re trekking through the desert on Route 111, you have to choose between the Root Fossil and the Claw Fossil. That’s a choice in both games. However, later in the game, the fossils you find in the "Mirage Forest" or "Mirage Mountain" change.
Omega Ruby players will find the Helix Fossil (Omanyte) and Claw Fossil (Anorith) more commonly.
Alpha Sapphire players tend to find the Dome Fossil (Kabuto) and Root Fossil (Lileep).
As for Mega Stones, most are available in both games, but they are tucked away in different spots. The biggest difference is the Aggronite and Tyranitarite. Aggron’s stone is exclusive to Alpha Sapphire’s Rusturf Tunnel, while Tyranitar’s stone is in Omega Ruby’s Jagged Pass. Since you can't even get Larvitar or Aron in certain spots without trading, this further pushes the "version" identity.
Does it actually matter in 2026?
Kinda. If you’re playing on original hardware, you have to consider that the Nintendo Network for 3DS has been shut down. You can’t just hop on the GTS (Global Trade Station) and swap a Zangoose for a Seviper anymore.
Local wireless still works. If you have a buddy with the opposite version sitting on the couch next to you, you’re golden. But if you’re playing solo, the Omega Ruby Alpha Sapphire version exclusives are now a permanent barrier to a 100% Pokédex.
Choose Omega Ruby if you prefer physical attackers and want a slightly more "standard" Pokémon experience with Groudon. Choose Alpha Sapphire if you like more technical playstyles, better defensive options like Latias, and a villain team that feels a bit more like a bunch of chaotic ruffians.
Your Next Steps for Hoenn Completion
- Check your local trading scene: Since online play is dead, look for local retro gaming groups or "StreetPass" revival meetups.
- Plan your Fossils: Don't just grab the first one you see in the desert; look at your team's type weaknesses first. Anorith (Bug/Rock) and Lileep (Grass/Rock) fill very different niches.
- Bank and Home: If you have Pokémon Bank installed, remember you can still move these exclusives up to modern games like Pokémon Scarlet or Violet, but you can't move them "down" or across to the opposite version without a second 3DS.
- The Delta Episode: Prepare your team for the post-game. Regardless of version, you’ll eventually face Rayquaza and Deoxys, but having your version-exclusive legendary (Groudon or Kyogre) trained up makes the transition into the endgame much smoother.