Brucellosis is known to cause reproductive disorders or abortions in terrestrial mammals, especially domesticated animals. The causative agent, Brucella is a gram-negative, facultative intracellular bacterium of genus Brucella. Recently Brucella infection has been reported in a variety of wild animals including marine mammals. In the western North Pacific, pathological and serological investigations suggested Brucella infection occurred in common minke whales (Balaenoptera acutorostrata). In the present study, infection with Brucella sp. was demonstrated in granular testes with caseation or calcification from the North Pacific whales using polymerase chain reaction (PCR). Previous studies showed that terrestrial and North Atlantic seal isolates have omp2a and omp2b gene copies at outer membrane protein 2 gene locus, while North Atlantic cetacean isolates have two omp2b gene copies. The North Pacific whale Brucella has been shown to have omp2a and omp2b gene copies at the locus in this study, suggesting the similarity to terrestrial and North Atlantic seal isolates. However, the sequence of omp2b was different from those of known Brucella strains, and formed a distinct clade in the phylogenetic tree of omp2 gene. The insertion of an IS711 transposable element downstream of bp26 gene is a common molecular feature to all marine isolates. The insertion was found in the North Pacific whale Brucella, suggesting its close relation to North Atlantic marine isolates. Furthermore, an identical DNA sequence, which is unique to North Atlantic seal isolates, was found in the North Pacific whale Brucella. These results together showed that the North Pacific Brucella was different from known Brucella strains, but was most similar to North Atlantic seal strains