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Background and Aim: Some medically important species of Muscidae and Fanniidae families are among synanthropic flies and can be seen in human habitats; therefore they can be mechanical vectors of different pathogenic microorganisms. Identification and determination of species of these flies is essential for any control program planning. This study was conducted to determine the faunal diversity of Muscidae and Fanniidae flies in Tehran, Iran. Methods and Materials: This was a cross-sectional descriptive and taxonomic study, conducted in 2 phases, during 1996-97 (pilot study) and 2000-2002 (complementary study) in Tehran and suburbs. Medically important flies were captured and identified. A net-hashing was used to capture adult flies by the direct observing method. To determine the fauna of flies in different habitats, 4 biotopes, including corpse (human, birds, livestock), garbage and decaying organic matter, animal carcasses, and human indoor habitat, were selected. Big hashing nets (95 cm in diameter) were used for capturing adult flies. Results: A total of 2418 adult flies belonging to 8 families of Muscidae, Fanniidae, Calliphoridae, Sarcophagidae, Tachinidae, Syrphidae, Conopidae, and Anthomyiidae were captured. Among these, 1279 belonged to the Muscidae and Fanniidae families. Four genera and 5 medically important species were identified from two families. Conclusion: Based on the existing scientific documentation, 2 species of M. stabulans and F. scalaris are reported for the first time from Iran. However, M. stabulans is a common species, the presence of which in Iran seemed probable. [ABSTRACT FROM AUTHOR]