Seawater sample from the coral reefs of the Kerama Islands of Okinawa were assessed for the presence of carotenoid-producing bacteria. Results of 16S rDNA analysis of the bacteria obtained from the isolated bacteria showed unique patterns that were different from those of the bacteria obtained from the ordinary marine area. Phylogenetic analysis revealed a slight correlation with the statistical analysis of the PDA chart patterns. The results suggest that useful materials for human health such as carotenoids can be extracted from many carotenoid-producing bacteria such as those found the coral reefs the Kerama Islands.