We obtained carotenoid-producing microorganisms at a high frequency from water samples collected at Misasa (Tottori, Japan), a region known for its high natural radioactivity content. A comprehensive 16S rRNA gene-based phylogenetic analysis revealed that the 104 potential carotenoid producers isolated from Misasa could be classified into 38 different species belonging to seven bacterial classes (Flavobacteria, Sphingobacteria, alpha-Proteobacteria, gamma-Proteobacteria, Deinococci, Actinobacteria, and Bacilli). Of these 38 species, 14 showed sequence similarities less than 97% to their closest identified relatives, and 9 were related to genera that have not been described earlier in terms of carotenoid production. The red-pigmented isolates belonging to Deinococci showed marked resistance to gamma rays and UV irradiation, while those related to Sphingomonas showed weak resistance. The carotenoids produced by the isolates were zeaxanthin (6 strains), dihydroxyastaxanthin (24 strains), astaxanthin (27 strains), canthaxanthin (10 strains), and unidentified molecular species that were produced by the isolates related to Deinococcus, Exiguobacterium, and Flectobacillus. UV irradiation would be useful for the selective isolation of carotenoid-producing microorganisms, and that new microbial producers and other molecular species of carotenoids may potentially be identified from radioactive environments.