In the present study, to the evaluate genetic diversity and genetic structure of a mutational rice (B810S) with a color marker from China, the entire sequence of the atpH gene of the chloroplast genome from B810S was amplified by polymerase chain reaction (PCR). The PCR products were sequenced, and sequence variations in the atpH gene were then examined. The entire sequence of the atpH gene was 245 bp in size. Compared it with 810S, whichis the male parent of B810S, the results showed a similarity of 51.22%. There are 2 haplotypes in their atpH gene sequences and the haplotype diversity and nucleotide diversity were 1.0000 and 0.41250, respectively. In addition, phylogenetic analysis of B810S and other normal rice strains was conducted and a phylogenetic tree was constructedusing maximum likelihood (ML) method based on the atpH gene sequence from the chloroplast genome. The results of phylogenetic analysis showed that B810S separated from other rice strains formed an independent branch in the phylogenetic tree, which suggests that B810S with a color marker is a new male sterile rice line. The molecular approach employed in this study provides a foundation for further study of the genetic diversity and structure of rices in different geographical regions of China and other regions in the world.