The genus Halidesmus is unique within the Congrogadidae in the possession of three lateral lines. The three species are described, diagnosed, and illustrated, and a key to the species is provided. One of these species, from Kenya, is described as new and is distinguished from the other two species in lacking scales on the cheek and nape, in having 11 suborbital pores, and in the degree of development and form of the lateral lines and associated pores. A tentative hypothesis of relationships is proposed, based primarily on lateral-line structure, relating H. scapularis to Halidesmus polytretus n. sp. as sister species together forming the sister group of H. thomaseni.