The use of color (as distinct from color pattern) in comparative evolutionary studies is important, and objective, independent characters are needed. A new method was employed to investigate geographic color variation in the small arboreal lizard Anolis trinitatis on the island of St. Vincent. The simple delta analysis (based on the difference between eigenvector coefficients for adjacent regions of the spectrum) is aimed at increasing the objectivity with which a spectrum is cut into independent segments and does not predetermine segment width or number. There are distinct habitat types within this small island and distinct phylogenetic lineages (based on a kilobase of cytochrome b sequence) within this species. A series of matrix correspondence (Mantel) tests indicate that aspects of color are associated with habitat type (e.g., green dorsum in rain forest lizards), molecular phylogeny, or both. Hence, both adaptation by selection and historical processes are implicated as causes of geographic variation in color. The dewlap variation (e.g., strong ultraviolet reflectance in some Atlantic coastal sites) is very pronounced and, contrary to some expectations, may result in reproductive isolation even within small Lesser Antillean islands.