In this study, organ samples from 426 common seals Phoca vitulina, 298 harbour porpoises Phocoena phocoena, 34 grey seals Halichoerus grypus and 10 other marine mammals were assessed for the presence of Brucella species. Forty-seven common seals, 2 harbour porpoises and 1 grey seal were found to be positive for these bacteria. A total of 91 Brucella strains were successfully isolated, due to the fact that Brucella spp. were found in more than one organ sample in 15 animals. The primary organ in which the bacteria were present was the lung. In addition, 2 strains were isolated from lungworms (Parafilaroides spp.). Forty-nine of the isolated strains were selected for further analysis using conventional phenotyping methods. Molecular characterisation was carried out by analysing the IS711 and omp2 loci. With respect to the distribution of the IS711 loci in the genome, the 49 field isolates differed strongly from the terrestrial Brucella species and marginally from the marine Brucella reference strain NCTC12890. Based on the results of the PCR restriction fragment length polymorphism (PCR-RFLP) investigation of the omp2 locus, the majority of the Brucella field isolates were classified as B. pinnipediae, recently proposed B. pinnipedialis, possessing 1 omp2a gene and 1 omp2b gene. Two field isolates revealed the presence of 2 omp2a genes, as has been described for Brucella ovis. To our knowledge, these results confirm for the first time the presence of Brucella species in the marine mammal population of the German North Sea. These findings highlight the need for additional research on the relevance of these Brucella species for marine hosts and their environment.