Arcobacter cryaerophilus is a heterogeneous species in which two distinct subgroups have been delineated by means of DNA-DNA hybridization experiments and whole-cell protein profile analysis. In the present study the taxonomic status of these subgroups was reassessed by using amplified fragment length polymorphism and heat shock protein 60 gene sequence analysis. The results demonstrate that A. cryaerophilus has a complex taxonomic structure which consists of multiple cores of strains that share intermediate levels of DNA-DNA hybridisation and that exhibit low levels of DNA-DNA hybridisation towards other Arcobacter species. One of these cores consisted of the majority of strains and included most but not all subgroup 2 reference strains previously reported. A. cryaerophilus subgroup 1 strains represented three distinct cores, among which the type strain occupied a distinct position. These results thus demonstrate that the use of the current subgroup nomenclature in A. cryaerophilus should be abandoned, and that the type strain is genetically aberrant and poorly represents strains belonging to this species.