Assuming you are talking about different hues instead of saturation (like the case with humans), mating strategies could be one. See the common side-blotched lizards
Edit: To speak more specifically, evolution is a game. All this means is that your strategies (behavior, anatomy, morphology, physiology) depend on how it compares to others. You are only as good as your neighbor and similarly only need to be slightly better. Basically, it's the old joke "I don't have to outrun the bear, I just have to be faster than you".
In games, we can quantify how good or weak a certain strategy is by comparing it against other strategies. Let's say we have the Dating Game. You're a male contestant vying against two others for the interest of the femal. To make this simpler, let's say there are two strategies a male contestant can be: confident but arrogant (CA), shy yet charming (SC). If the CA male always wins against SC no matter the context, then it is called a dominant strategy. (If all contestants are the same, then its just a roll of the die) In this case, it is in the best interest of every contestant to come off as CA and soon all male contestants will act that way. The strategy-to-play table looks like this
Other 2 You
CA CA Play CA
CA SC Play CA
SC SC Play CA
Let's say though that in when two CA male contestants meet, they get into a testosterone fight, try to outcompete each other and just lose any attraction to the female. In a case like this, the third SC guy comes off as the better partner since he doesn't partake in the machismo. The strategy-to-play table is now
Other 2 You
CA CA Play SC
CA SC /
SC SC Play CA
(In the mixed case, there is no best strategy to play because you will automatically be the loser). In this case, we have what is known as the rare-strategy advantage. Essentially, it says play the opposite of what everyone else is play. In this case, there can be two outcomes which are essentially the same: a mixed state where there is half CA, half SC; or a constant flip-flop between the two. Regardless though, both strategies are preserved in the population.
In your case, the rare coloration may be more attractive to the opposite sex (male or female) for some unknown reason that preserves their status in the population.
