The Vibrio vulnificus CMCP6 genome harbors nine copies of divergent large subunit (LSU) rRNA genes that may express and constitute four kinds of LSU rRNA molecules in a single cell. Primer extension analyses showed that these heterogeneous LSU rRNA transcripts are all expressed and assembled into ribosomes during both infection and nonpathogenic stages. Phylogenetic analyses of the internal transcribed spacer between SSU and LSU genes indicated that rRNA operons of V. vulnificus CMCP6 can be clustered into three distinct groups in rRNA genes of closely related Vibrio species. These findings imply that divergent rRNA genes in V. vulnificus CMCP6 resulted from interspecies recombination events in V. species, while the consequences of expression of heterogeneous rRNA molecules are not clear.