This is similar to my branching species thread but not quite.
There's a possibility that your species has a lot of genetic diversity and can come in different color varieties or morphotypes. The color of the organism you are controlling will obviously be decided by you in the editor but npc's that are the same species could have minor differences like slightly different colors, longer fins etc. A good example are guppies. Guppies can come in a wide range of colors and fin shapes. Some have lyretails while others have fantails or swordtails. Despite different fin shapes and different colors these guppies are the same species. Another good example is us human beings. Some of us have dark skin while others have lighter skin. We have different color hair and eyes too. This could be procedural in the game.
In order to survive, you must look to the stars for an answer.