Onchocerciasis, or river blindness, is caused by infection with Onchocerca volvulus, a filarial parasite which infects about 40 million people in Africa and Latin America. Epidemiological, clinical, entomological and serological studies of African onchocerciasis led to the hypothesis that Onchocerca volvulus exists in different forms in the forest and savannah. It is uncertain if these differences are due to genetic differences within O. volvulus itself, or to epigenetic factors, such as differences in the host populations. To date no basic biochemical differences between the forest and savannah populations of O. volvulus has been found, although isoenzyme studies have shown that differences in allele frequency between forest and savannah populations exist. Here we describe the isolation of a DNA sequence that seems to be specific for the forest form of O. volvulus, the first indication of a basic genetic difference between the savannah and forest forms.