Two morphologically similar fish tapeworms, Proteocephalus exiguus and P. percae, were differentiated by the random amplified polymorphic DNA (RAPD) marker and Southern-blot hybridization techniques. Four geographic isolates of P. exiguus and two of P. percae were studied using eight arbitrary decamer oligonucleotides as primers. Species-specific RAPD fragments enabled reliable separation of the taxa studied. Generally, 1-3 fragments specific for P. percae and 1-4 P. exiguus-specific fragments were detected using individual primers. Intraspecific differences in P. percae depended on the primer used. The profiles generated by the primers OPA 04 and OPA 12 showed an intraspecific variation, whereas six other primers tested revealed indistinguishable banding patterns. On the other hand, intraspecific variability of P. exiguus, detected among four geographic isolates, was evident using all primers. Additionally, the utilization of two species-specific RAPD markers as effective probes was demonstrated. Distinct differences between P. exiguus and P. percae were revealed using each of the restriction enzyme/probe combinations.