Abstract Background Having the right identification is essential in the field of entomology. The scanning electron microscopy allows rapid and accurate identification of different species of flies since a better visualization of the external morphology of immature and some adults is possible. The aim of this study is to describe some ultrastructures of three flies in the Mesembrinellidae family: Mesembrinella bellardiana; Mesembrinella bicolor and Mesembrinella semihyalina, all examined by scanning electron microscopy to help increase the anatomical database on flies and deal with phlylogenetic implications. Results The flies were examined under JEOL 6390LV scanning electron microscope (SEM). The microtrichia morphology of the antennae is similar to that of other and are present on all antennal surface with variable distribution. The chaetic sensilla were observed only in the scape (chaetic sensilla I) and pedicel segments (chaetic sensilla I-III). Three types of sensilla: trichoidea, basiconic and clavate were observed in the first flagellomere of M. bellardiana; and two types of sensilla: trichoidea and basiconic were noticed in M. bicolor and M. semihyalina. Olfactory pits were observed in both gender of M. bellardiana and female of M. bicolor . The maxillary palp of the Mesembrinella species in this study does not show sexual dimorphism. Conclusion This investigation provided new findings of some diagnostic structures of flies using SEM, since many of them could have not been observed just by the use of light microscopy.