The study investigated the transfer and the stability of the S. intermedius flora in three bitches and their puppies. A total of 240 cutaneous and mucosal isolates of S. intermedius was collected from three healthy Cavalier King Charles spaniels and their puppies during the immediate prepartum period and after whelping, over a total of 15 weeks. The isolates were genotyped with random amplified polymeric DNA-polymerase chain reaction analysis (RAPD-PCR) using two primers. Seventeen different genotypes of S. intermedius were identified. One or two of the genotypes were dominant in each of the bitches and their puppies. The rest were isolated only once or twice from the bitches or their puppies. The study indicates that S. intermedius flora within each studied bitch mainly consisted of one or two dominating and persistent clones, which were transferred from the dam to her puppies immediately after birth.