Knowledge of the Oestroidea and Muscoidea fauna of Greece and Cyprus remains fragmentary, with substantial parts of the two countries having never been systematically surveyed. The present study verifies the presence of Scathophaga stercoraria (Linnaeus, 1758) in Cyprus and records 16 new species from Greece, belonging to five calyptrate families: [Anthomyia illocata Walker, 1856 (Muscoidea: Anthomyiidae); Scathophaga lutaria (Fabricius, 1794) (Muscoidea: Anthomyiidae); Fannia pallitibia (Rondani, 1866); Fannia pusio (Wiedemann, 1830) (Muscoidea: Fanniidae); and Coenosia sp. nov. 1, Coenosia sp. nov. 2, Lispe flavicincta Loew, 1847, Lispe nuba Wiedemann, 1830, Lispe orientalis Wiedemann, 1824, Lispe cf. sericipalpis (Stein, 1904), Potamia littoralis Robineau–Desvoidy, 1830 (Muscoidea: Muscidae); Apodacra radchenkoi Verves and Khrokalo, 2015, Craticulina tabaniformis (Fabricius, 1805), Miltogramma rutilans Meigen, 1824, Nyctia lugubris (Macquart, 1843) (Oestroidea: Sarcophagidae), and Linnaemya lithosiophaga (Rondani, 1859) (Oestroidea: Tachinidae)]. These records are based on the examination of 152 dry-pinned specimens from 58 localities, collected between 1978 and 2026 across Greece and Cyprus using a combination of passive (animal-baited traps, UV-bright pan traps) and active (hand collecting, net sweeping) sampling methods, together with insect material from the entomological collections of the National Museum of Natural History Goulandris and the Melissotheque of the Aegean. In addition, the first checklists of the family Fanniidae and the subfamily Scathophaginae for Greece and Cyprus are presented. Collectively, the findings presented expand the documented diversity of Greek and Cypriot Calyptratae and refine the current understanding of their biogeographic patterns, providing an updated framework for taxonomic, ecological, forensic, and other applied entomological research within the two countries.