Acinetobacter baumannii is a troublesome bacterial pathogen which can cause life-threatening disease states in humans. In recent years, infections caused by A. baumannii have become extremely difficult to treat due to its ability to acquire or upregulate antimicrobial resistance determinants. Although individual virulence factors for this pathogen are known, the regulation mechanisms controlling these genes are not well understood. One widely employed regulatory mechanism that bacteria, including A. baumannii, have adopted is through two component signal transduction systems (TCSTS), which are comprised of two proteins; a membrane-bound histidine kinase and a cytosolic response regulator. Eleven TCSTS can be identified in A. baumannii ATCC 17978 and the adeRS system was selected as the focus of this study. In many A. baumannii isolates adeRS controls expression of the adeABC multidrug efflux pump, which provides resistance to a multitude of antimicrobial agents. An adeR A. baumannii ATCC 17978 deletion mutant (∆adeR) was generated and subsequently compared to the parent in a number of studies. The impact of this deletion was assessed transcriptomically by RNA sequencing revealing that upon adeR deletion, the transcriptional levels of more than 180 genes were altered ≥2-fold. As expected, in ∆adeR adeAB was up-regulated, but surprisingly, resistance profiles only exhibited minor fold-changes to some of the known substrates of adeAB when compared to the parent strain. Examination of resistance in ∆adeR to a larger set of compounds identified an 8-fold decrease in resistance to the antimicrobial diamidine compound pentamidine. This resistance could be partially restored by the re-introduction of a wildtype copy of adeR, or by the addition of ferrous iron. Thus, a new role for the AdeRSAB system has been identified and further details of the manner by which adeRS interacts with genes involved in pentamidine resistance may help understand how this bacterium can evade current therapeutic treatments.