Elucidating the ultimate and proximate mechanisms of melanistic color pattern formation has become an important focus of evolutionary biology. There are relatively few studies, however, examining the composition and architecture of pigment cells in melanistic reptiles. The typical color pattern of the skink Plestiodon latiscutatus, which inhabits the Izu Islands and Izu Peninsula of Japan, consists of brown dorsal coloration, five vivid yellowish white stripes, and a blue tail (in juveniles). We have observed melanistic morphs at a low frequency (<0.05%). Based on a histological examination of pigment cells, we determined that the melanistic morph of P. latiscutatus collected from Shikine in the Izu Islands possesses only dermal melanophores and lacks the xanthophores and iridophores seen in the normal coloration. This arrangement of pigment cells differs from the only other studied melanistic lizard, Sceloporus undulatus, in which the dark skin of the melanistic morph results from a simple increase in the density of melanophores relative to xanthophores and iridophores. Our findings indicate that associations between color pattern phenotypes and the expression of candidate color genes, such as Mc1r, are more complex than previously assumed; coloration in reptiles is controlled not only by cellular processes related to single pigment production but also by the differentiation of multiple pigment cells.