Before you read, note that this page is dedicated to the affiliations of different races and not information about the races themselves and what ships they pilot. For more information on races, visit the page dedicated to them found here.
The rebels are the primary antagonists of FTL. They are rebelling against the Federation for currently unknown reasons, and have almost destroyed the Federation. As you progress through the sectors in FTL, you will be pursued by a rebel fleet which will follow you as you play. If you are caught by the rebel fleet, you will have to fight an elite fighter, which is a more powerful version of the rebel fighter. The most powerful enemy in FTL is the Rebel Flagship, which is also the final boss.
Rebel ships can be identified by an orange hull and blue stripes. They sometimes have drones. There are also ships known as auto-scouts, which are ships built by the rebels to scout ahead of the fleet. They have no oxygen room and therefore no crew, so boarding is inadvisable with these ships. They are identified by dark gray paint. Elite fighters can be found if the rebel fleet overtakes a beacon you are currently waiting at.
The Federation is composed of a group of races united in the galaxy to pose a great strength in numbers and are the main protagonists in FTL. You start as a Federation ship carrying information which is vital to the survival of the Federation, and must progress to the eighth sector to deliver it to the commander of the Federation fleet. It is known that the Federation treats races with equality, though the Slugs were discriminated against within it, allegedly on account of their secretive and conspiratorial character.
Federation ships have a white hull with orange stripes. Unlike other ships, Federation ships are only interacted with in distress beacon events and found as pirate ships.
Other than rebels, space pirates are the most common enemies found in sectors. Pirates are groups of outlaws in the galaxy who aim only to earn power and money, and almost always resort to violence to acquire it. In certain events, you will have to rescue a ship which has been commandeered by pirates.
Pirates ships appear as normal ships. However, they have crudely painted purple markings on the hull and often have a smaller but more diverse crew than the normal ship would have otherwise. For instance, on a Slug pirate ship, there can be a Rock and a Zoltan for crew, instead of Slugs.
Mercenaries are similar to pirates, but they do not use violence to acquire what they want unless they are attacked first. You will sometimes find a mercenary ship which you can pay to slow the rebel fleet's pursuit down or update your map with information on the sector. Alternatively, you can attack and destroy the mercenary ship or leave them alone.
Mercenary ships have the same markings as pirate ships, and also have a diverse crew.
Slavers are considered by most to be the worst form of criminal. Slavers will find weak ships, take crew members from them, and enslave them. These slaves are sold off to other ships for a sum of money. If encountered, you can buy a slave. You will be able to choose from three races what this slave will be. You can also attack the ship or leave it alone. Sometimes, when you are attacking the ship, they will surrender and offer you a slave as tribute. If you have available space it is advisable to accept this.
Again, slaver ships have the same markings as pirate ships.
Civilians are people who don't really take either side and just want to stay out of the war. They have their own forces that defend them, however, they aren't heavily armed.