Flesh flies are important in forensic investigations as their larvae can estimate the post-mortem interval (PMI) in human remains. However, before using life-history traits as evidence, correct species identification is necessary. Flesh flies also transmit enteropathogens to humans as diarrheal diseases and cause myiasis in cattle. Identifying adult flesh flies is challenging due to their similar appearance, and it is primarily based on male genitalia morphology. Therefore, studying the phylogenetic relationships within this group is necessary. In this study, a phylogenetic analysis of 23 species representing 9 subgenera of the genus Sarcophaga from Egypt was conducted. It involved 56 external morphological and male genitalia characteristics. The results revealed that Helicophagella and Heteronychia clades are monophyletic groups, while Liopygia and Liosarcophaga clades are paraphyletic groups. The remaining subgenera consist of a single species each, known as monotypic groups. The study also supported sister group relationships between Sarcophaga and Helicophagella subgenera, Liopygia and Phytosarcophaga subgenera, and Bercaea and Liosarcophaga subgenera. The results revealed different groupings and supported sister group relationships between certain subgenera. Morphological and male genitalia characteristics played a significant role in species differentiation. Overall, these traits serve as reliable indicators for studying variation among Sarcophaga species.