To develop tools to analyse parasitic nematode population structures and the effects of selection pressure on the nematode population, we isolated and characterised 13 microsatellite markers of the nematode Haemonchus contortus. The density of CA/GT microsatellites, once in 575 kb, is lower than in mammals. Although the isolated CA/GT repeats were imperfect, the majority of the microsatellites were polymorphic in one or more populations. An extensive genetic diversity both within and between populations could be established Two-thirds of the CA/GT microsatellites were followed by a variable number of 128 bp direct repeat elements, HcREP1. HcREP1 is a repetitive element in the H. contortus genome, which is homologous to the repetitive TcREP element in the nematode Trichostrongylus colubriformis.