The phylogenetic affinities of the melanistic subspecies Trachylepis sulcata nigra have never been investigated, and it was unclear if this subspecies represented a locally adapted population or a distinct species. Sequences from the nuclear marker RAG-1 (1149 bp), two novel rapidly-evolving nuclear markers KIF24 and EXPH5 (554 bp and 941 bp respectively), and the mitochondrial gene ND2 (1056 bp) were analysed from 84 individuals of T. s. sulcata and two individuals of T. s. nigra. Additionally, the range of T. s. nigra was estimated using museum records, and correlations between environmental variables and the occurrence of melanism were explored. Molecular analyses depict T. s. nigra as nested within a strongly monophyletic T. s. sulcata, suggesting this population is not genetically isolated or distinct. We therefore recommend T. s. nigra be synonymized with T. s. sulcata. The best predictor of melanism along the coastline in this population is a high number of fog days per year, a finding consistent with studies of melanism in cordylid lizards in southern Africa. Further sampling may determine gene flow levels occurring across the contact zone of melanistic and non-melanistic phenotypes and provide insight into selective forces maintaining this trait.