Molecular population-genetic analysis has revealed that for several human diseases, including tuberculosis, plague and shigellosis, the generally accepted taxonomic status of the organisms involved does not fit the usually accepted genus or species criteria. This raises the question of what species concept to apply to bacteria. We suggest that the species definition in bacteria should be based on analysis of sequence variation in housekeeping genes, and also that the ‘clone' be given official status in bacterial nomenclature. This will allow demotion of the species or genus status of several traditionally recognized human pathogens, but retention of current names of anomalous species and genera as clone names.