Background: Clinal variation is defined as gradual variation in a character associated with geographic distance among sites. Microlophus atacamensis is a medium large lizard species which inhabits the intertidal zone of northern Chile, distributed from Antofagasta (23° 39′ S) to Arrayán, La Serena (29° 41′ S) in a gradient which could show clinal variation. Geometric morphometrics analyzes differences in shape independent of size; information about shape allows a more complete biological interpretation than information on morphological variation. This study evaluated clinal variation in the head shape of M. atacamensis from five localities (Antofagasta, Paposo, Pan de Azúcar, Caldera, and Tres Playitas) using dorsal and lateral views, comparing form variation with latitudinal distribution. The heads of adults collected were photographed in lateral and dorsal views. Results: The analysis did not find significant differences in form among the five localities, in contrast to the proposal of earlier studies, and no differences were recorded between the sexes. Possible reasons why these populations are not differentiated in the latitudinal gradient are discussed. Conclusions: Our results show that there are no differences between the studied, among the explanations are that populations of this species are subjected to similar environments that promote convergence of the structures analyzed.