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Molecular data support two distinct species of Nilotanypus Kieffer (Chironomidae: Tanypodinae) differentiated on morphology in all stages. Each is described as Nilotanypus haplochelus new species and Nilotanypus ctenochelus new species respectively. Morphological differentiation is stronger in the larva and pupa, with adult stages less well differentiated, as seems usual in the genus. Both species are distributed widely across the Australian continent, but seemingly absent from offshore islands and Tasmania. A tendency towards lotic psammophily (sand-dwelling) is evident, with sympatry at some tropical / subtropical locations. Additional molecular data from non-Australian taxa indicates that N. ctenochelus is sister to all other sampled taxa and N. haplochelus to an undescribed species from oriental China. Review of all stages of several non-Australian species requires revised generic diagnoses, and, critically, recognition of Pentaneura comata Freeman 1953 as synonymous with the type of the genus, Nilotanypus remotissimus Kieffer 1923 (new synonym).
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