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<p>Abstract</p> <p>Background</p> <p>The ParA/Soj and ParB/Spo0J proteins, and the <it>cis</it>-acting <it>parS </it>site, participate actively in chromosome segregation and cell cycle progression. Genes homologous to <it>parA </it>and <it>parB</it>, and two putative <it>parS </it>copies, have been identified in the <it>Mycobacterium bovis </it>BCG and <it>Mycobacterium smegmatis </it>chromosomes. As in <it>Mycobacterium tuberculosis</it>, the <it>parA </it>and <it>parB </it>genes in these two non-pathogenic mycobacteria are located near the chromosomal origin of replication. The present work focused on the determination of the transcriptional organisation of the ~6 Kb <it>orf60K-parB </it>region of <it>M. bovis </it>BCG and <it>M. smegmatis </it>by primer extension, transcriptional fusions to the green fluorescence protein (GFP) and quantitative RT-PCR.</p> <p>Results</p> <p>The <it>parAB </it>genes were arranged in an operon. However, we also found promoters upstream of each one of these genes. Seven putative promoter sequences were identified in the <it>orf60K-parB </it>region of <it>M. bovis </it>BCG, whilst four were identified in the homologous region of <it>M. smegmatis</it>, one upstream of each open reading frame (ORF).</p> <p>Real-time PCR assays showed that in <it>M. smegmatis</it>, mRNA-<it>parA </it>and mRNA-<it>parB </it>levels decreased between the exponential and stationary phases. In <it>M. bovis </it>BCG, mRNA-<it>parA </it>levels also decreased between the exponential and stationary phases. However, <it>parB </it>expression was higher than <it>parA </it>expression and remained almost unchanged along the growth curve.</p> <p>Conclusion</p> <p>The majority of the proposed promoter regions had features characteristic of <it>Mycobacterium </it>promoters previously denoted as Group D. The -10 hexamer of a strong <it>E. coli </it>σ⁷⁰-like promoter, located upstream of <it>gidB </it>of <it>M. bovis </it>BCG, overlapped with a putative <it>parS </it>sequence, suggesting that the transcription from this promoter might be regulated by the binding of ParB to <it>parS</it>.</p>