Diptera Mesembrinellidae present great ecological importance as potential bioindicators and Calliphoridae stand out for their medical-sanitary importance as potential vectors of pathogens and causes of human and animal diseases such as myiasis. They beneficially aid in elucidating crimes in forensic entomology, contributing to determine the postmortem interval (PMI) and assisting in the healing process of necrotic wounds in larval therapy. This study aimed to inventory the Calliphoridae and Mesembrinellidae fauna in order to evaluate structural parameters and to apply faunal indexes in catching species in the Itaipu–Piratininga lagoon complex, in Niterói (Rio de Janeiro), Brazil. The collections were carried out monthly from September 2015 to August 2016 with fish bait (sardines) exposed for 48 h, totaling six traps installed in three physiognomies (mangrove, ombrophilous forest, and restinga). In total, 9,773 individuals were captured, divided into two families, five genera, and 11 species. Chrysomya megacephala (Fabricius, 1794) was the predominant species, while Mesembrinella bellardiana (Aldrich, 1922) was the least representative species, indicating the preservation level of this ecosystem. Ombrophilous forest was the physiognomy with greater diversity and restinga was the physiognomy with greater species dominance. The similarity index indicated greater similarity among the mangrove and restinga populations.