Natural pigments are normally products of complex biosynthesis pathways where many different enzymes are involved. Corals and related organisms of class Anthozoa represent the only known exception: in these organisms, each of the host-tissue colors is essentially determined by a sequence of a single protein, homologous to the green fluorescent protein (GFP) from Aequorea victoria. This direct sequence-color linkage provides unique opportunity for color evolution studies. We previously reported the general phylogenetic analysis of GFP-like proteins, which suggested that the present-day diversity of reef colors originated relatively recently and independently within several lineages. The present work was done to get insight into the mechanisms that gave rise to this diversity. Three colonies of the great star coral Montastraea cavernosa (Scleractinia, Faviida) were studied, representing distinct color morphs. Unexpectedly, these specimens were found to express the same collection of GFP-like proteins, produced by at least four, and possibly up to seven, different genetic loci. These genes code for three basic colors-cyan, green, and red-and are expressed differently relative to one another in different morphs. Phylogenetic analysis of the new sequences indicated that the three major gene lineages diverged before separation of some coral families. Our results suggest that color variation in M. cavernosa is not a true polymorphism, but rather a manifestation of phenotypic plasticity (polyphenism). The family level depth of its evolutionary roots indicates that the color diversity is adaptively significant. Relative roles of gene duplication, gene conversion, and point mutations in its evolution are discussed.