Dewlap coloration of anoles is diverse and both carotenoid and pterin pigments play a role in generating this color variation. In the present study, we examined the carotenoid and pterin concentrations responsible for generating color variability in the proximal, central, and marginal dewlap sections in three subspecies of Anolis jubar of the Cuban southern coast (A. j. oriens, A. j. maisiensis, and A. j. albertschwartzi). With the exception of pterins—likely drosopterins—(entirely absent in A. j. albertschwartzi and in the scales proximal to the dewlap base in the three subspecies), the dewlap colors were produced by the combination of the two pigment classes. Carotenoid levels differed by section in A. j. oriens and A. j. maisiensis, being highest in the central section of dewlap. Anolis j. oriens had higher pterin concentration than A. j. maisiensis in both central and marginal sections. Carotenoid concentrations were significantly higher than pterin concentrations, excepting the central section of A. j. oriens, in which no significant differences were found between pigments. Our findings demonstrate subspecies-level variation in dewlap pigmentation in Cuban A. jubar and have implications for cellular mechanisms responsible for phenotypic variation.