The genomic variability of sixty-nine populations of the potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis from Europe and South America were analyzed using the RAPD-PCR technique with sixty-six 10-mer primers. Large genomic differences were found between the two PCN species (i.e. 33%). The genomic pool of British G. pallida populations showed considerably less variation than the Peruvian populations, with 73% and 41% similarity between populations respectively. The genomic similarity among populations of G. rostochiensis was 89% for UK populations and 82% when the two continental European populations were included. Nevertheless, between populations within each species and from the same locality, genomic differences were still found. The RAPD-PCR technique proved to be useful for revealing the genomic variability between and within species using DNA extracted from 50 cysts, but it gave variable results when DNA extracted from individual females or cysts was used, suggesting that for evaluating the genomic variability of individuals it is better to use specific primers. RAPD-PCR was also used successfully to distinguish the two PCN species, individuals selected and selected for virulence and even biotypes using individual cysts. Based on the results found when comparing biotypes of Globodera pallida, it is suggested that all the biotypes considered in the International Pathotype Scheme could be grouped into Pa1 and Pa2/3 when classifying European populations, and Pa1A or Pa1B, P4A, P5A and P6A when analyzing South American populations. However, these groupings should be regarded just as a reference, because virulence bioassay results plus the data found using the RAPD-PCR technique suggested that, at least in G. pallida, virulence seems to be a polygenic trait ruled by several genes with additive effects. On the other hand, based on the same sort of data, virulence in G. rostochiensis seems to be ruled only by major genes. Selected and unselected populations of G. pallida, reared on either potato clone Solanum vernei (VTn)2 62.33.3 or a susceptible control, were distinguished using the RAPD-PCR technique and primers Operon A-07, E-06, G-16 and I-05. Three of the fragments that appeared to distinguish the unselected from the selected populations were cloned into an isolate of E. coli and their sequences obtained. Gpalpha, seems to be part of a promoter region of a gene probably related or linked to virulence. The use of differential clones to characterize PCN populations with different proportions of each virulence gene is a valuable tool. Whilst diagnostic probes for routine identification of virulent populations are being developed, the use of the “gene pool similarities” concept involving the DNA patterns of standard populations as genetic virulence types (i.e. virulence biotypes), integrated with information on their response to differential clones bearing genes for resistance, would represent the best approach towards devising a sustainable control strategy to optimize the usefulness of whatever resistance is available.