To delimit the distribution of matrilines of the black iguana (Ctenosaura pectinata), detect potential contact zones between them, and test the hypothesis of geographic concordance in the structuring of matrilines with respect to genetic structuring across the nuclear genome. Pacific coast of Mexico in the states of Nayarit, Jalisco, Colima, Michoacán in the lowlands adjacent to the western end of the Mexican Volcanic Belt. Tissue samples were obtained every 10–20 km along a transect across the range of three previously described mitochondrial DNA (mtDNA) clades of C. pectinata. Iguanas were genotyped with 11 nuclear microsatellites and maternal lineages were inferred based on mtDNA sequences. Geographic structure and geographic concordance between biparentally and maternally inherited markers were analysed with clustering methods, FST and NST indexes as well as haplotype networks. Geographic structure was evident for both markers and the existence of contact zones confirmed. Nevertheless, the distribution of nuclear and mtDNA genetic variation is not geographically concordant. Four matrilines exist in the area, whereas only two nuclear clusters occur. A contact zone between nuclear clusters extends along a distance of c. 60 km, and introgression is evident in individuals from several localities. High levels of genetic diversity were detected on the western coast of Mexico. Historical and contemporaneous processes seem to shape the distribution of genetic variation in C. pectinata. There are no evident geographic, environmental or ecological barriers that coincide with genetic subdivisions, and the observed mtDNA structure is likely to be the result of past climatic changes. The less structured distribution of nuclear genetic variation is consistent with the homogenizing effect of male-biased dispersal. Our findings have implications for the taxonomy and conservation strategies for this threatened species, and highlight the fact that geographic analyses of both cytoplasmic and nuclear genetic variation are important for the meaningful inference of evolutionary and demographic histories.