CTnDOT is a 65-kb conjugative transposon present in Bacteroides spp. that confers resistance to erythromycin [erm(F)] and tetracycline [tet(Q)]. An interesting feature of CTnDOT is that both excision from the chromosome and transfer of CTnDOT are stimulated by exposure to tetracycline. However, when no tetracycline is present, transfer of CTnDOT is not detectable. Previous studies suggested that a region containing a small RNA, RteR, appeared to mediate repression of CTnDOT transfer; however, virtually nothing was known about RteR. We have demonstrated that RteR is a 90-nucleotide transcript that is not further processed. RteR inhibits conjugative transfer of CTnDOT by targeting the transfer region, a 13-kb operon that encodes the tra genes required to assemble the mating apparatus. We report here that RteR interacts with the region downstream of traA. Levels of the downstream tra mRNA are dramatically reduced when RteR is present. Further, RteR does not appear to decrease the half-life of the tra mRNA transcript, suggesting that RteR does not bind to the transcript to initiate RNase-dependent decay, similar to other trans-acting small RNAs. We predict that RteR may act to enhance termination of the tra operon within traB, which could account for the decreased abundance of the tra transcript downstream of traA and explain why the tra mRNA has the same half-life whether or not RteR is present. RteR is the only small RNA that has been characterized so far within the Bacteroidetes phylum.