Aichi virus (AiV), a member of the genus Kobuvirus in the family Picornaviridae, causes gastroenteritis in humans. It was noted that AiV differs from other picornaviruses in its unusually high C content and a very high degree of genome-ordered RNA secondary structures. However, the genetic variability and mutational restrictions on a full-genome scale have not been studied. In addition to the available five complete AiV genomes, we determined here another five complete coding sequences of AiV sampled in Germany, 2004. Distinctive AiV genetic features included a low incidence of recombination along the genome without obvious hotspots or spared regions and very low rates of synonymous and non-synonymous variation supporting an absence of AiV serotypes. In addition, the absence of recombination between AiV genotypes A and B suggested the existence of reproductively isolated taxonomic units below the species level.