The genotypic diversity of isolates belonging to dominant Bacillus species in raw milk from conventional and organic dairy farms in Belgium was investigated using (GTG)(5) PCR. Three different clusters could be identified in the Bacillus subtilis group, reflecting the intraspecific heterogeneity within this collection of strains. For Bacillus cereus, one predominant type could be detected, indicating a common contamination source or a type that is best capable of contaminating the raw milk. For Bacillus licheniformis, two predominant types were found, that could not be linked to the origin, season or temperature of isolation. The largest diversity was found in the Bacillus pumilus species. Still, one cluster comprising two subclusters could be noticed, that. separated isolates from conventional and organic farms. This study indicates that there is a large difference in the population structure of various important Bacillus species in raw milk. (c) 2007 Elsevier Ltd. All rights reserved.