ABSTRACTThe population structure of theBacillus cereusgroup (52 strains ofB. anthracis,B. cereus, andB. thuringiensis) was investigated by sequencing seven gene fragments (rpoB,gyrB,pycA,mdh,mbl,mutS, andplcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in theplcRtree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. TheplcRgene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of theplcRgene may be frequent. The homogeneity ofB. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.