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Notodiaptomus cannarensis sp. n. is described from a reservoir on the Amazonian slope of the Ecuadorian Andes. The new species is unique among diaptomid calanoid copepods in the display of hypertrophied, symmetrical wing-like extensions at each side of the female composite genital somite. Furthermore, it displays a female urosome reduced to only two somites due to the incorporation of abdominal somites III and IV to the composite genital double-somite, and a male right fifth leg with the outer spine of second exopodal segment recurved and implanted proximally on margin. It differs from any other Notodiaptomus in the display of a large rectangular lamella on proximal segment of exopod of male right fifth leg. The species is currently known only from Mazar reservoir, a eutrophic water body placed above 2127 m a.s.l. on the River Paute (Cañar Province; southern Ecuador), where it is the most common crustacean in the water column.