An unidentified Helicobacter species, strain MIT 01-6451, was frequently detected in mice obtained from domestic commercial and academic institutions in Japan. To partially characterize this strain, its distributions in the gastrointestinal tract and hepatobiliary system of mice were investigated. In gastrointestinal tissues, this strain was detected in all cecum, colon, and feces samples tested, whereas fewer mice were positive in the ileum, jejunum, and duodenum. Interestingly, strain MIT 01-6451 was also detected in most stomach samples and in 33% of gallbladder samples. One mouse was found to be infected with multiple Helicobacter species. Fourteen copies of 16S rRNA genes were cloned from the tissues of this mouse. One had the highest level of sequence homology with H. canadensis, while 13 had the highest level of homology with the H. ganmani type strain or strain MIT 01-6451. Twelve of these 13 16S rRNA genes were mosaic sequences, being partially derived from H. ganmani and strain MIT 01-6451. These results suggest that H. ganmani and Helicobacter sp. MIT 01-6451 are prevalent in specific-pathogen-free mouse colonies in Japan and that lateral gene transfer probably occurs among Helicobacter species during coinfection.