Mycobacteria are thought to have either one or two rRNA operons per genome. All mycobacteria investigated to date have an operon, designated rrnA, located downstream from the murA gene. We report that Mycobacteriun fortuitum has a second rrn operon, designated rrnB, which is located downstream from the tyrS gene; tyrS is very close to the 3 end of a gene (3-mag) coding for 3-methylpurine-DNA-glycosylase. The second rrn operon of Mycobacterium smegmatis was shown to have a similar organization, namely, 5 3-mag-tyrS-rrnB 3. The rrnB operon of M. fortuitum was found to have a single dedicated promoter. During exponential growth in a rich medium, the rrnB and rrnA operons were the major and minor contributors, respectively, to pre-rRNA synthesis. Genomic DNA was isolated from eight other fast-growing mycobacterial species. Samples were investigated by Southern blot analysis using probes for murA, tyrS, and 16S rRNA sequences. The results revealed that both rrnA and rrnB operons were present in each species. The results form the basis for a proposed new scheme for the classification of mycobacteria. The approach, which is phylogenetic in concept, is based on particular properties of the rrn operons of a cell, namely, the number per genome and a feature of 16S rRNA gene sequences.Mycobacterium tuberculosis and Mycobacterium leprae are major human pathogens which have the ability to grow slowly within host cells. The mechanisms used by these pathogens to control their growth rates is not well understood. Cell growth is dependent on protein biosynthesis, which, in turn, requires the synthesis of new ribosomes. The rate-determining step in ribosome synthesis is thought to be the rate of synthesis of rRNA (4,8). Therefore, there is a need to identify factors important to transcription of rRNA (rrn) operons (12,14) and the ways in which these transcripts are processed to form mature rRNA (16,17).Traditionally, mycobacteria are classified as either slow growers or fast growers according to the time taken (less than 7 days for fast growers, longer than 7 days for slow growers) for colonies to appear on a solid medium (15, 37). The slowgrowing pathogens M. tuberculosis (6,18,36) and M. leprae (20,21,32) have a single rrn operon per genome, whereas most fast growers have two rrn operons per genome (2, 9). The apparent correlation between growth rate and the number of rrn operons per genome provides a possible explanation for the division of mycobacteria into fast-and slow-growing species.However, slow-growing and fast-growing mycobacteria are all close relatives, as judged by the relatedness (95% or more) of their 16S rRNA sequences (26,29,35), so that comparative studies provide a way of identifying highly conserved sequence elements important to the synthesis of mature rRNA (13). Furthermore, it is valuable to identify the gene immediately upstream from the rrn operon under investigation (11, 13). First, this upstream gene serves to identify the operon. Second, upstream gene sequences may provide elements dedicated to the ex...