The slow-growing, nontuberculous mycobacteriumMycobacterium kumamotonensepossesses two rRNA operons,rrnAandrrnB, located downstream from themurAandtyrSgenes, respectively. Here, we report the sequence and organization of the promoter regions of these tworrnoperons. In therrnAoperon, transcription can be initiated from the two promoters, named P1rrnAand PCL1, while inrrnB, transcription can only start from one, called P1rrnB. Bothrrnoperons show a similar organization to the one described inMycobacterium celatumandMycobacterium smegmatis. Furthermore, by qRT-PCR analyses of the products generated from each promoter, we report that stress conditions such as starvation, hypoxia, and cellular infection affect the contribution of each operon to the synthesis of pre-rRNA. It was found that the products from the PCL1 promoter ofrrnAplay a pivotal role in rRNA synthesis during all stress conditions. Interestingly, the main participation of the products of transcription from the P1 promoter ofrrnBwas found during hypoxic conditions at the NRP1 phase. These results provide novel insights into pre-rRNA synthesis in mycobacteria, as well as the potential ability ofM. kumamotonenseto produce latent infections.