A set of 48 Lactobacillus isolates recovered from the faecal swabs of different dog breeds in Andhra Pradesh were genotyped by (GTG)5 repetitive element PCR (rep-PCR). The genomic fingerprinting allowed us to differentiate five major clusters among the 48 canine faecal Lactobacillus isolates viz. cluster I (8 isolates), cluster II (6 isolates), cluster III (14 isolates), cluster IV and V (10 isolates each). The discriminatory power of rep-PCR for Lactobacillus species was found to be 0.997. Rep-PCR cluster analysis data was compared with the previous results of Lactobacillus group-specific PCR. Perfect matches occurred between these data, as evidenced by the correspondence of dendrogram clustering patterns with that of group-specific PCR patterns. This was the first report on application of rep-PCR for the genotyping of lactobacilli of dog faecal origin in India.