Darwin's theory of natural selection can also explain many types of coloration. This theory is based on the following facts: 1. there is variation between individuals, 2. some of this variation is heritable, and 3. resources are limiting. It follows that if variants are better able to survive or obtain resources, these variants will be favored over time. For example, individuals may survive better (may be selected) because they are immune to a disease, are able to escape predators, or are particularly good competitors for food. The result of this selection is organisms that are well adapted for foraging for food, evading predators, or fighting disease.

For example, look at the horned lizard on the left. Its coloration blends in well with its surroundings. The tan parts of its back are a good match for the rocks it lives amongst. The black bands on its back break up its outline so it looks less like a lizard and more like a rock. It even adopts a rock mimicking behavior in which the lizard hunches up its back and stays very still. One can easily imagine that different individuals differ slightly in the amount of tan color that they have on their backs. Should one shade or amount of tan be slightly more cryptic, individuals with that coloration will face less predation and will be naturally selected.

Natural selection for organisms that are camouflaged seems eminently reasonable. But how do we explain animals that have bright coloration that seems designed to stand out? One way to explain it is by sexual selection, that individuals with bright coloration have been favored because they gained increased the reproductive success. However, natural selection can explain some cases of bright coloration because sometimes it may be advantageous to not be camouflaged.

For example, consider the marvelous salamander on the right. The bright yellow on its back seems designed to stand out to predators, especially against the contrasting black color. In fact, this salamander's coloration is the result of selection for bright coloration. This salamander is poisonous (it will ooze noxious liquid from the black lumps on its sides if you harass it). The bright colors of this salamander advertise that it is poisonous to predators. After all, it makes sense to let a predator know you are poisonous before you are attacked and killed!