This study investigated the morphometric variation in Melipona scutellaris stingless bees rational hive boxes from five states, inserted into the natural range of the species occurrence in northeastern Brazil. The cluster analysis (UPGMA) showed three distinct groups by determining the cutoff point. The multivariate analysis were performed using MANOVA and Canonical Variables for the shape analysis. The One-Way ANOVA was used to assess differences in centroid size. The results showed population divergence between localities limited by geographical barriers or great distances, corroborating previous observations by the UPGMA. Variation between colonies inter-state was higher that intra-state and, in most cases, Geometric Morphometrics was effective in identifying the origin of colonies transported to other states, observed in the cross-validation analysis that showed more than 70% of classification accuracy. Geometric Morphometrics could be used to evaluate the introduction of colonies within the kindred meliponary. Natural populations of Melipona scutellaris show a significant variation, which brings important implications to meliponiculture and to conservation strategies for this endangered species.