External organs associated with the male gonopore are described for 29 species covering for the first time all seven currently acknowledged, extant families of the orders Lophogastrida, Stygiomysida, and Mysida, and all ten subfamilies of the Mysidae (Mysida). The gonopores are located throughout on the structures of the coxa of the eighth thoracopods. The three orders are consistently differentiated based on their male genital characteristics. Species of the Stygiomysida genera Stygiomysis (Stygiomysidae) and Spelaeomysis (Lepidomysidae) share a closing apparatus formed by two laminar lobes flanking the genital orifice, an anterior setose lobe, and a posterior bare lobe; no tubular penes are developed. In contrast, the Lophogastrida are characterized by a bare, slot-like orifice without lobes; also, in this taxon, no tubular penes are developed. The gonopore is on the inner wall of the coxa without conspicuous elevation in the species of Eucopia (Eucopiidae) and Lophogaster (Lophogastridae) and on the top of an anvil-like elevation in Paralophogaster (Lophogastridae), or of a dome-shaped elevation in Gnathophausia and Neognathophausia (Gnathophausiidae). In all examined species of the Mysida, the gonopores show a closing apparatus formed by lobes; one or more of these lobes is setose in most species. Within the Mysida, the genus Hansenomysis (Petalophthalmidae) and most subfamilies of the Mysidae have well-developed paired penes with (sub) terminal orifice. Only Rhopalophthalmus (Rhopalophthalminae) lacks penes but has bilobate gonopores located without additional elevation at the inner distal corner of the strongly enlarged coxa of the eighth thoracopods; this coxa contains a large seminal vesicle. Within the variety of external male genitalia in the Eumalacostraca, the structures associated with the gonopores appear to be plesiomorphic in Lophogastrida. In the Mysida, they appear to be apomorphic and support the monophyly of this order with respect to the previously published, competing phylogenetic trees. This requires additional evidence in the case of the Stygiomysida.