Understanding the degree of genetic population differentiation is important in conservation genetics for inferring gene flow between populations and for identifying small and isolated threatened populations. We evaluated the genetic variation within and between three populations of the rock firefinch (Lagonosticta sanguinodorsalis), a range restricted firefinch endemic to Nigeria and Cameroon. The populations were closely located (c. 100 km apart) within the species' core distribution in Central Nigeria. We found that the populations had similar levels of gene diversities (H (E) ) and low but significant inbreeding coefficients (F (IS) ). Despite the short distance between populations there was a weak but significant population structure, which indicates that the populations are somewhat isolated and affected by drift within the species' core distribution in Nigeria. The knowledge of the genetic status of the rock firefinch will serve as a foundation to future studies to help understand population demography and for managing and maintaining viable populations.