Large-bodied ectoparasites are often observed only in low numbers in the field. How such rarely found parasites persist and maintain viable populations has been an intriguing question inadequately addressed. The simplest hypothesis is the existence of distribution hot spots, and another, but not mutually exclusive, possibility is a form of metapopulation structure where local populations are effectively connected via dispersal. In this study, we conducted an intensive epidemiological survey of a piscicolid leech Taimenobdella amurensis to elucidate spatial population structure and potential dispersal of this rarely found parasite. Four years of potential-host screening (n = 20 664) from 28 tributaries and 10 main stem reaches in a mountain river system of Hokkaido, northern Japan, revealed that occurrences of T. amurensis (n = 1348) were confined to spring-fed tributaries. Since most spring-fed tributaries were small (<1 km in length), it would seem to be unlikely for the ectoparasite to form a persistent local population in each tributary. The main host fish was Dolly Varden charr, which is known to disperse among neighbouring tributaries. These findings suggest that, along with the host, the ectoparasite displays a potential metapopulation structure, in which host-dependent dispersion may overcome local extinction by keeping the local populations connected.