There are six playable factions in Pandora: First Contact:
- Divine Ascension This faction is meant for early game rushes.
- Imperium This faction has a strong military throughout the campaign.
- Noxium Corporation This faction has a very strong economy.
- Solar Dynasty This faction can create large powerful cities.
- Terra Salvum This faction is good at avoiding combat.
- Togra University This faction excels at research.
One additional faction was added in Pandora: Eclipse of Nashira:
- The Ambassadors This faction excels at diplomacy and espionage.