The genome of the Pseudomonas putida strain KT2440 contains five paralogous proteins (TurA, TurB, TurC, TurD and TurE) of the H-NS-like MvaT class of transcription regulators. TurA and TurB belong to groups I and II, respectively, both containing orthologous MvaT proteins that are present in all Pseudomonadaceae species. On the contrary, TurC, TurD and TurE belong to group III, which contains species-specific paralogous MvaT proteins. We analysed the global effects on the P. putida KT2440 transcriptome of eliminating the conserved TurA and TurB proteins, which had been identified in our previous studies aimed to search for novel specific co-regulators of the upper TOL operon for toluene biodegradation. While the loss of TurA de-repressed the expression of many genes covering a broad range of functional classes in both mid-exponential and early stationary phases, the absence of TurB brought about a very different outcome. Although the loss of TurB affected also very different functions, the number of genes that changed in the turB mutant was fivefold smaller than that of TurA. Furthermore, TurB does not act generally as repressor. Interestingly, the degree of overlap between their mutual regulons is very limited. A closer examination of one case where such overlap clearly occurs (a gene cluster for biosynthesis of lipodepsinonapeptide phytotoxins) revealed that TurA and TurB can act in concert, perhaps by forming a heterodimer. In addition, our results indicate that TurA is the master regulator of TurB as well as of the other paralogues, TurD and TurE.