An intimate linkage between the regulation of biofilm formation, stress tolerance and genetic competence exists in the dental caries pathogenStreptococcus mutans. ThercrRPQgenes encode ABC exporters (RcrPQ) and a MarR-family transcriptional repressor of thercroperon (RcrR) that play a dominant role in the regulation of the development of genetic competence and connect competence with stress tolerance and (p)ppGpp production inS. mutans. Here we identify the target for efficient RcrR binding in thercrpromoter region using purified recombinant RcrR (rRcrR) protein in electrophoretic mobility shift assays and show that DNA fragments carrying mutations in the binding region were not bound as efficiently by rRcrRin vitro. Mutations in the RcrR binding site impacted expression from thercrRpromoterin vivoand elicited changes in transformation efficiency, competence gene expression, and growth inhibition by competence-stimulating peptide; even when the changes inrcrRPQtranscription were minor. An additional mechanistic linkage of RcrR with competence and (p)ppGpp metabolism was identified by showing that the rRcrR protein could bind to the promoter regions ofcomX,comYAandrelP, although the binding was not as efficient as to thercrRPQpromoter under the conditions tested. Hence, tightly controlled autogenous regulation of thercrRPQoperon by RcrR binding to specific target sites is essential for cellular homeostasis, and RcrR contributes to the integration of genetic competence, (p)ppGpp metabolism, and acid and oxidative stress tolerance inS. mutansthrough both direct and indirect mechanisms.