Anolis onca is a lizard species located in the Araya peninsula, in northern Venezuela. Populations of this species may have been isolated in the late Cretaceous and later recombined during the Quaternary through a new isthmus by sedimentary processes. To test this assumption, in five populations of A. onca , starch gel electrophoresis was used to estimate genetic variability within populations, interpopulation differentiation (F ST ), and gene flow (N e m). Additionally, under the premise of genetic differentiation between subpopulations under the isolation by distance (IBD) model, we conducted a phylogenetic analysis for five subpopulations of this lizard. Increases of genetic distance values (D) between subpopulations arranged consecutively between the Chacopata and Guayacán locations and a clear structuration as estimated by the F ST parameter, evidence isolation by distance as indicated by the IBD model. However, N e m values did not conform to this model, suggesting that the subpopulations, although actually connected, may have been shaped by independent evolutionary processes. The two clades resulting from the phylogenetic analysis do not group populations closer geographically since clade B (Chacopata+Istmo Sur) lies in areas geologically ancient whereas clade A [(Istmo Centro+Istmo Norte)+Guayacán)] occupies areas of recent sedimentary origin. It is thus reasonable to infer that other factors besides the geographical distance between subpopulations may have also conditioned the structure found.