Melipona mandacaia is a stingless bee species responsible for the pollination of many native plants in Brazil, South America. In spite of its ecological and economic importance, natural populations of M. mandacaia have been depleted because of deforestation. In order to evaluate the interpopulation morphometric structure of remaining populations, we carried out geometric morphometric studies based on fore wing shape in this native bee species. The grouping analysis by UPGMA revealed three distinct clusters and significant differences in fore wing size were observed (p<0.001) among populations. The three groups were also reflected in the first two principal components explaining about 60% of the total variation. These results indicate differentiation among populations, which can be regarded as unique management units. Therefore, efforts should be directed to the conservation of local populations of M. mandacaia to avoid the negative impacts of loss in pollination over plant species and environmental services.