Mycobacterium tuberculosis harbors four mce operons. Among them, mce2 operon is preceded by a FadR-like regulator mce2R (Rv0586). Here, we report the operator sites of the mce2R and its orthologs in other sequenced mycobacteria and non-mycobacterial species Nocardia farciana. All the identified DNA motifs illustrate the FadR subfamily specific nucleotide preference. Moreover, these motifs from the upstream region share sequence conservation, which is in agreement with the similarity of their DNA binding domain. Using electrophoretic mobility shift assay, we demonstrate that the predicted DNA motifs specifically interact with the recombinant Mce2R-Rv0586. Our present study has implications in the understanding of cis-regulatory elements and the auto-regulatory nature of the FadR subfamily of regulators.