A total of 29 subspecies of B. thuringiensis strains previously used to raise 28 standard antisera, were differentiated using PCR fingerprinting with primers derived from the Repetitive Extragenic Palindrome (REP) sequence. Using REP specific primers (REP2-1 and REP3) in a defined PCR condition, a reproducible fingerprinting pattern in the size range of 300 2,000 bp was obtained. The bacterial strains can be distinguished by comparing fingerprint patterns. The dendrogram of the fingerprints revealed that the B. thuringiensis subspecies fell into four major clusters with a level of similarity of approximately 20%. The relatedness of the REP-PCR fingerprint patterns of most B. thuringiensis subspecies did not correlate with the bacterial classification based on flagella serotyping. The REP-PCR fingerprint method should prove to be a rapid and simple tool for numerical taxonomic analysis of B. thuringiensis strains.