In order to understand the habitation conditions of the bacteria of the genus Legionella in Noyu （unattended natural hot springs in mountains and fields） in Japan, isolation of Legionella spp. was attempted in the Noyu samples from 11 prefectures nationwide between May and September 2012, and the following results were obtained. Overall, Legionella spp. was isolated from 16 of 43 samples （37.2%）. The species was isolated from the Hokkaido region to the Chugoku region but not from the Shikoku region to the Kyushu region. The number of bacteria detected was usually small, less than 5.0×10¹ CFU/100 ml, as found in 11 samples （68.8%）, while counts of 10² or more to 10³ or less CFU/100 ml were found in two samples （12.5%）. Legionella pneumophila was the most commonly found strain, with 19 strains （90.5%） found, and was the dominant species. Regarding the serogrouping, four strains （21.1%） fell under group 1, the most common grouping, followed by three strains （15.8%） in group 3, two strains （10.5%） in group 5, etc. Moreover, the detected bacterial strains other than L. pneumophila included two strains （9.5%） of L. londiniensis. The temperature of the Noyu from which Legionella spp. was isolated was between 33.1°C and 41.5°C with a pH ranging from 5.2 to 8.1. The present report is the first report to clarify the habitation conditions of strains of Legionella spp. isolated from Noyu in Japan.