Abstract Darkling beetles (Tenebrionidae) are a diverse and ecologically significant group, particularly in arid environments, yet their taxonomy remains problematic due to scarcity of phylogenetic contributions and robust morphological investigations. This study applies 3D geometric morphometrics to evaluate the taxonomic validity and morphological differentiation among three closely related sandworm beetle taxa: Gonopus deplanatus, G. tibialis kalaharicus, and G. tibialis punctatus. Seventy-nine museum-preserved specimens were digitized using a 3D scanner, with multiple scans taken from six different orientations to ensure comprehensive surface reconstruction. Twenty-one anatomical landmarks were assigned to the prothorax (12 landmarks) and pterothorax (9 landmarks), targeting significant taxonomic features like pronotal width, elytral curvature, and the structure of the prosternal process. Based on this dataset, the size and shape variation were analyzed. Results suggest that G. t. punctatus displayed a narrower pronotum and more pronounced prosternal process than G. t. kalaharicus and G. deplanatus, indicating a previously underappreciated taxonomic distinction. For elytra, the differences among taxa were primarily observed in width, curvature, and declivity. Additionally, the stronger correlation between pterothorax shape and size suggests that larger individuals tend to have more pronounced and rounded elytra, potentially influencing thermoregulation or structural reinforcement in response to environmental pressures. These results show the transformative potential of 3D geometric morphometrics in entomological systematics by providing a quantitative framework for distinguishing closely related beetle taxa. These findings suggest that traditional taxonomic criteria may have underestimated the extent of variation between these taxa, underscoring the importance of integrating advanced morphometric approaches into systematic studies. Furthermore, detecting allometric influences in shape variation provides new insights into potential functional and ecological adaptations, which may be linked to the distinct desert environments these beetles inhabit.