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Abstract Representatives of the genusAnncaliiaare known as natural parasites of dipteran and coleopteran insects, amphipod crustaceans, but also humans, primarily with immunodeficiency.Anncaliia algerae‐caused fatal myositis is considered as an emergent infectious disease in humans.A. (=Nosema, Brachiola) algerae, the best studied species of the genus, demonstrates the broadest among microsporidia range of natural and experimental hosts, but it has never been propagated inDrosophila. We present ultrastructural analysis of development ofA. algeraein visceral muscles and adipocytes ofDrosophila melanogaster2 wk after per oral experimental infection. We observed typical toAnncaliiaspp. features of ultrastructure and cell pathology including spore morphology, characteristic extensions of the plasma membrane, and presence of “ridges” and appendages of tubular material at proliferative stages.Anncaliia algeraedevelopment inD. melanogasterwas particularly similar to one ofA. algeraeandA.(Brachiola) vesicularumin humans with acute myositis. GivenD. melanogasteris currently the most established genetic model, with a fully sequenced genome and easily available transgenic forms and genomic markers, a novel host–parasite system might provide new genetic tools to investigate host–pathogen interactions ofA. algerae, as well to test antimicrosporidia drugs.