There have been some investigations carried out about necrophagous flies and their biodiversity indices in Iran. In the present study, the species composition of flies, their richness, and biodiversity were investigated in central Iran. In a cross-sectional study, specimens were collected monthly in three different climate areas of Qom Province. Species diversity, species richness, and species evenness were calculated to estimate the species biodiversity of flies. In total, 7,291 flies were collected and identified using valid identification keys that classified flies into four families and 15 different species. The largest collection of flies was obtained in the mountainous areas comprising 36.2% of specimens. Moreover, five forensically important species of fly were collected in this region with the potential to cause human and animal myiasis: Calliphora vicina, Lucilia sericata, Musca domestica, Wohlfahrtia nuba, and Chrysomya albiceps. There were slight differences in species richness and diversity indices in the areas. In mountainous areas, the Shannon–Wiener index and richness were maximum (H' = 1.87, S = 13). The evenness based on the Shannon evenness index in the mountainous areas was 0.728 and 0.719 in desert areas, whereas it was the highest (0.764) in the semidesert areas. Moreover, high values of the Jaccard similarity index were observed in captured necrophagous fly species in all the areas. The necrophagous fly fauna and species diversity indices were high because of an increase in the evenness. In general, some well-known forensically important species of flies were collected that proved the potential of myiasis occurrence in this area.