The shape of organisms is determined by a complex interplay of mechanisms that promote variation and those that drive selection, such as purifying selection, which can reduce variation. However, other factors beyond selection may contribute to the conservation of certain morphologies across species. Certain traits can be highly conserved, complicating species identification, while others may vary between populations or individuals, particularly in geographically isolated populations with restricted gene flow. Populations spread across “habitat islands”, such as coastal dunes, present an opportunity to study variation in shape. Along the Pacific coastal dunes of Mexico’s Baja California peninsula, two non-sister species of the honeypot ant genus Myrmecocystus are found, which are indistinguishable using current dichotomous keys. In this study, geometric morphometric methods were applied to search for intra- and interspecific morphological variation. Additionally, the question arises whether the geographical separation of the ants has contributed to intraspecific variation of shape. Geometric morphometrics for 105 individuals of the two species were analyzed from the head in frontal, and the mesosoma in dorsal view. Based on the results, the shape of the head is different for the two species, and intraspecific variation was also detected between some of the populations. The shape variation of the mesosoma was more conserved between species, showing overlap. Therefore, while the coastal dune species of Myrmecocystus are similar in appearance, there are variations in shape that allow for their delimitation, as well as morphological plasticity within species, which may be due to natural variation and/or local adaptations.