In most Hymenoptera, the caste differentiation is influenced by differential environmental cues (e.g., food), which affect larvae development. However, Melipona stingless bees represent an exception to this rule. Workers and queens can emerge from brood cells of the same size, with the same quantity and quality of food. The different phenotypes of female bees depend on the interaction of genetic and environmental components. This mechanism is driven by the juvenile hormone, a key physiological factor synthetized by the corpora allata glands. In addition to that, epigenetic mechanisms were recently associated with caste development in Melipona scutellaris . In this study, using images captured by confocal microscopy and analyzed by 3D computational reconstruction, we show the similarities and differences in the pattern and volume of heterochromatin in the cell nuclei of corpora allata glands of M. scutellaris . Our results imply that heterochromatin territorial dispersion may act as a major player on the female phenotypic plasticity of M. scutellaris stingless bees.