Historically, studies evaluating morphological diversity in stingless bees (Hymenoptera, Apidae: Meliponini) by geometric morphometrics have been used to successfully discriminate taxa and/or populations. Moreover, the use of geometric morphometrics to evaluate phylogenetic morphological variation among stingless bee species has received less attention. Here, we used geometric morphometrics to assess taxonomic discrimination and putative phylogenetic signals for six diapausing stingless bee species (Plebeia) occurring in southern Brazil. In all, 12 landmarks were captured from forewings of P. droryana, P. saiqui, P. emerina, P. remota, P. nigriceps and P. wittmanni. Our data show that the centroid size of the forewings reliably discriminated, for example, between P. droryana and P. emerina from P. saiqui. Moreover, this trait does not have a significant phylogenetic signal. In turn, we found that the overall accuracy in discriminating between the six Plebeia species according to forewing shape was 84%, while the confusion matrix achieved 71%. Interestingly, our discriminant analysis separated Plebeia species nesting in tree cavities from those nesting under granitic rocks. The latter group has second cubital (landmarks = 5, 6, 7), first medial (landmarks = 2, 3, 8) and first submarginal cells (landmarks = 3, 4, 9, 10) that are larger than those of species nesting in trees. The forewing shape showed a strong phylogenetic signal, therefore suggesting that its variation may be due to an evolutionary history shared between Plebeia species studied here rather than to environmental features. This work sheds light on the value of forewing size and shape attributes in discriminating Plebeia species within same genus. We suggest that landmarks separating different taxonomic groups could be incorporated into dichotomous keys to help in identifying clades of complex resolution.