In basicly all 4X games it's a single race
Though, the reason these games (I'm mostly thinking Master of Orion, here) equate race and empire is because there are other empires in the game, and race (i.e. appearance and abilities) is an easy way of distinguishing them.
I'll invoke the Rule of Personification Conservation to describe this. (That's a link to TV Tropes, by the way, so don't click on it if you're not free for the rest of the day.) The rule suggests that if a character isn't human, there should be a good reason for it. There are still a couple of non-reasons that work -- you could add in a few token aliens, just to make your galaxy seem bigger and less human-centric, or you could purposely reject this trope, and add alien races willy-nilly.
But supposing that you want to follow the rule, here are a few options that spring to mind:
- One species per empire - each faction of the game is composed of one race. Normally, each faction will gain certain perks based on their race's biology and culture. This also tends to make certain races natural allies, and others natural enemies. Personally, I despise this trope, but it is the most common way of doing things.
- Certain factions are multi-racial - Some factions are composed of multiple races, possibly to demonstrate their tolerance for other species and points of view. If not, it's probably because the faction works by one of the paradigms I list below.
I get the impression that the player of your game isn't supposed to be ruling one empire among several (a la Master of Orion, Civilization, Alpha Centauri, etc.), but is trying to manage a single, monolithic empire, whose only enemies lie within its borders. In that case, the rule applies a bit differently; here are some examples:
- Xenofiction - you remove humans from the game, wholesale, or just push them off to the side because you want to make a point of the fact that your characters don't act like humans. If you don't think that humans would form a galaxy-spanning absolute monarchy like you want, you could just make them aliens, and claim that that's the way their brains are wired up (as I said in my earlier post).
- One species per province - different regions of the galaxy are populated by different species. In this case, the player will associate each race with its particular needs. So for example, if the space-elves and space-dwarfs hate each other, the player will have to get them to cooperate, and make sure that neither one feels that the other is getting a better deal.
- One species per function - different species are traditionally given different types of work, based on what (popular belief thinks) they are best suited to. Parallels can be drawn to traditional gender roles or to a caste system. If you need to highlight a character's rebellious nature, you could show them doing a job that isn't traditional for their species.
- Master and slave races - certain species -- especially robots -- get the short end of the stick, and are (almost) always seen in servitude or doing menial labor. Naturally, the master race will believe that this arrangement is actually "one species per function", and that the slave race is more suited to slavery, while the master race is suited towards leadership. The key difference between this one and the last one is that the master race is clearly better off. If you have a race of priests, a race of politicians, a race of warriors, and a race of artists, which one has the higher status? But if you have one race that runs things and another that does them, it's a bit more obvious.