The species Aegla schmitti is relatively abundant in epigean streams in the Upper Ribeira Basin, southeastern Brazil and has a few records in caves. In this study, we questioned if those individuals would be an accidental presence or could be populations already established in cave streams? In this case, would morphological variations be associated with superficial and subterranean stream reaches? In this exploratory survey we tried to answer these questions by assessing the shape variation of cephalothorax using landmark-based geometric morphometrics. Different shapes were found for both environments, evidencing a successful hypogean colonization. The area effect was discarded as being the unique factor responsible for the divergence, therefore, for the first time in the literature, here we report morphological modifications associated with subterranean colonization in troglophiles. We also conceived and discussed some hypotheses about the colonization.