Larval characters are of importance in systematic and evolutionary studies of Diptera but lag behind characters of adults due to difficulties in obtaining relevant information. Larvae of stomach bot flies are obligate parasites completing development exclusively in the alimentary tract of equids and rhinoceroses. They possess diversified morphological adaptations, providing remarkable examples to further our understanding of larval evolution. Herein, three-dimensional structures of first instar Gasterophilus pecorum and Gyrostigma rhinocerontis are compared using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). We suggest CLSM has a large potential for exploiting cryptic character systems of micro fly larvae, as spectral range and intensity of autofluorescence emitted by sclerotized structures and soft tissues are distinct, presenting a high-contrast mechanism for multistructural visualization with non-destructive sample preparation. Five new potential synapomorphies are proposed to corroborate the sister-group Gasterophilus and Gyrostigma. The upward curving mouth-hooks of first instar Gasterophilus and Gyrostigma are distinctive in Cyclorrhapha and possibly serve to facilitate the larval subcutaneous migration within the host. Three types of mouthhooks are recognized in first instar Oestridae, with the gently curved and gradually tapered type optimized as the ancestral state, from which the gasterophiline and hypodermatine types evolved independently.