Paragyrodactylus variegatus n. sp. (Monogenea: Gyrodactylidae) is described from the fins and body surface of Homatula variegata (Dabry de Thiersant, 1874) living in cold-water streams in the Qinling Mountains of central China. It represents the third known species in the genus, with all species parasitizing Asian river loaches (Cypriniformes: Nemacheilidae). The new species resembles most closely Paragyrodactylus iliensis Gvosdev and Martechov, 1953, but is diagnosed by its marginal hooks being longer than 19 μm, a sickle longer than 4 μm, a sickle aperture shorter than the sickle distal width, and absence of a ventromedial indentation in the haptoral accessory hard part. Scanning electron microscopy reveals a central foramen in the haptoral accessory hard part, and small knob-like protuberances on the heel and toe of the marginal hook sickle. A partial 18S (448 bp) and complete ITS-1, 5.8S, and ITS-2 (1,139 bp) rDNA sequences are provided. A preliminary phylogenetic analysis based on the partial 18S gene, which included all sequenced genera of the Gyrodactylidae, suggests P. variegatus n. sp. is basal within Gyrodactylus sensu lato. It is proposed that the genus is a relict freshwater lineage parasitizing river loaches in the mountain plateaus of central Asia.