Atherigona is a genus of flies in the family Muscidae.

Pests: Larvae of some Atherigona species are important pests in cultivation of cereals, like rice and maize. Many are known as shoot flies. Some important species include:

• Atherigona approximata (pearl millet shoot fly): affects Pennisetum typhoides, Sorghum bicolor
• Atherigona atripalpis (foxtail millet shoot fly): affects Setaria italica
• Atherigona biseta: affects Setaria italica, Setaria viridis
• Atherigona falcata (barnyard millet shoot fly): affects Echinochloa colona, Echinochloa frumentacea, Echinochloa stagnina, Panicum sumatrense
• Atherigona hyalinipennis (teff shoot fly)
• Atherigona miliaceae (finger millet shoot fly or little millet shoot fly): affects Panicum miliaceum, Panicum sumatrense
• Atherigona naqvii (wheat stem fly): affects Triticum aestivum, Zea mays
• Atherigona orientalis (tomato fly or pepper fruit fly)
• Atherigona oryzae (rice shoot fly): affects Oryza sativa, Paspalum scrobiculatum, Triticum aestivum, Zea mays
• Atherigona pulla (proso millet shoot fly): affects Panicum miliaceum, Panicum sumatrense, Paspalum scrobiculatum, Setaria italica
• Atherigona punctata (Coimbatore wheat stem fly): affects Triticum aestivum
• Atherigona reversura (bermudagrass stem maggot): affects Cynodon dactylon (turf grasses)
• Atherigona simplex (kodo millet shoot fly): affects Paspalum scrobiculatum
• Atherigona soccata (sorghum shoot fly): affects Sorghum bicolor, Zea mays, Eleusine coracana

Species: The following 299 species are recognized by Pont & Evenhuis, 2026: