How do certain characteristics of organisms, such as sex or species, and certain ecological factors, such as interaction with congeneric individuals, influence the variability of body architecture in an environmental setting over a small spatial scale? Using geometric morphometrics we performed a morphological comparison of the dorsal surface of the carapace of a congeneric guild formed by Aegla araucaniensis, A. denticulata denticulata, and A. abtao. Additionally, we evaluated whether the segregation of microhabitat by congeneric interactions generates variations in the shape of the cephalothorax in A. araucaniensis, comparing a population belonging to the congeneric guild with a close population without congeneric interactions. Changes in cephalothoracic shape are regulated primarily by intrinsic factors, such as the differences between species and sex of individuals. In addition, the congeneric interactions do not affect the expression of the carapace shape in either of the populations of A. araucaniensis. The patterns of variation in cephalothoracic architecture are similar to previous reports based on geometric morphometrics, traditional morphology and descriptive morphology. The interspecific variations are caused mainly by the configuration of the spinous processes at the borders of the carapace, while the variation due to sexual dimorphism is due to an expansion of the longitudinal axis in males and the caudal end of the carapace in females. Morphological responses in A. araucaniensis differ from previous comparisons made with other species of Aegla under similar environmental contexts but over distinct spatial scales. We discuss the sexual dimorphism from an adaptive perspective and propose that the architecture of the cephalothorax in aeglids is a trait conserved and regulated significantly throughout the evolutionary history of the group.