Fascioliasis is of well-known veterinary importance and an increasing human health problem, with reported cases in the five continents. The causative agents, Fasciola hepatica and Fasciola gigantica, present geographical distributions, which overlap in many regions of Africa and Asia, and in which the differentiation of both species is usually difficult because of the many variations in their morphological characteristics. Moreover, in humans, liver fluke classification cannot be achieved by clinical, pathological, coprological or immunological methods. The differential diagnosis between F. hepatica and F. gigantica infection is very important because of their different transmission and epidemiological characteristics. A simple and rapid PCR-restriction fragment length polymorphism (RFLP) assay, using the common restriction enzymes Ava II and Dra II, is described to distinguish between both fasciolid species. It is based on a 618-bp-long sequence of the 28S rRNA gene recently obtained from liver fluke populations of South America, Europe and Africa. This sequence showed a few nucleotide differences between both fasciolids and no intraspecific variations within each species. This assay provides unambiguous results and may be useful for both individual subject diagnosis and epidemiological surveys of humans and animals in endemic regions of sympatry.