We have previously characterized a Tc1-like transposable element Hctc1, from the parasitic nematode Haemonchus contortus. Here we describe the genetic variation of Hctc1 insertion sites in H. contortus populations differing in geographical origin, resistance to chemotherapeutics and level of inbreeding. Clear differences between populations were observed on Southern blots with a Hctc1-specific probe. Sequencing the 5'- or 3'-flanks of individual Hctc1 integration sites allowed the design of PCR reactions between a Hctc1-specific primer and the flanking regions. This revealed a considerable variation of integration sites of Hctc1 both within and between populations, although several integrations were shared by populations of different geographical origin. For four of the eight markers allele frequencies were shifted during selection for resistance to chemotherapeutics and/or inbreeding. For two positions both the 5' and 3' regions flanking Hctc1 were isolated and PCR showed that for these two positions the variation of transposon associated markers between populations were indeed caused by variation in integration of Hctc1. For these two positions co-dominant markers were developed. These results indicate that Hctc1 insertions may serve as genetic markers for H. contortus.