Genotyping methods have been developed and applied to differentiate Campylobacter jejuni isolates over the last two decades. Although a wealth of information was generated, the data are disappointingly complex and do not support simple models of transmission. Several observations have apparently weakened the value and complicated the interpretation of genotyping methods. For several methods, instability of genotype has been demonstrated, due to recombinations with or without transformation. C. jejuni is partly non-clonal, as demonstrated by multilocus sequence typing, which is explained by a natural ability to take up DNA. Plasticity of the genome, allowing for recombinations involving large DNA segments, and recombinations within loci frequently used for typing, further complicates the interpretation of typing data. The lack of clear-cut epidemiologic trends is probably not due to a lack of data or paucity of the used techniques, but is caused by the complex population genetics of the species.