To increase the existent genetic variability in cysteine proteases, a polymorphism study was performed in Haemonchus contortus by comparing 2 different strains of the parasite: North American (NA) and Spanish (SP) strains. For this purpose, the polymorphism of 5 previously reported genes (AC-1, AC-3, AC-4, AC-5 and GCP-7) were analysed by PCR–SSCP and sequencing procedures. Based on the SSCP results, a total of 20 different alleles were identified for the 5 loci assessed. Except locus AC-5, all the loci were polymorphic. Loci AC-1, AC-3, AC-4 and GCP-7 showed 5, 8, 2 and 4 alleles, respectively. The allelic frequencies ranged from 0·0070 to 0·8560 and were significantly different between strains. In addition, nucleotide diversity analyses showed a significant variation within and between strains. The variations in the nucleotide sequence of the different alleles were translated in some cases into changes in the amino acid sequence. Evidence of genetic variability in cysteine proteases from two different strains of H. contortus for the same set of genes had not been previously reported.