The genus Bartonella contains Gram-negative arthropod-borne bacteria that are found in many small animal reservoirs and are capable of causing human disease. Bacteria utilize a general stress response system to combat stresses from their surrounding environments. In α-proteobacteria, the general stress response system uses an alternate σ factor as the main regulator and incorporates it with a two-component system into a unique system. Our study identifies the general stress response system in the α-proteobacterium, Bartonella henselae, where the gene synteny is conserved and both the PhyR and alternate σ factor have similar sequence and domain structures with other α-proteobacteria. Furthermore, we showed that the general stress response genes are up-regulated under conditions that mimic the cat flea vector. We also showed that both RpoE and PhyR positively regulate this system and that RpoE also affects transcription of genes encoding heme-binding proteins and the BadA adhesin. Finally, we also identified a histidine kinase, annotated as BH13820 that can potentially phosphorylate PhyR. In addition, analysis of the transcriptome from the Houston-1 strain of B. henselae by RNA-Seq reveals a family of small RNAs (termed Brt1-Brt9 for Bartonella Regulatory Transcripts 1-9) that may rapidly adapt gene expression patterns to the diverse hosts of this bacterium. This family of RNAs consists of nine novel, highly expressed intergenic transcripts, ranging from 193-205 nucleotides with a high degree of homology (70-100%) and stable predicted secondary structures that are unique to the genus Bartonella. Northern blot analysis indicates that transcription of these sRNAs was highest under conditions mimicking those of the cat flea vector (low temperature, high hemin). The predicted promoters for Brt1-Brt9 have been cloned upstream of a β-galactosidase reporter gene in pNS2 to identify conditions altering transcription. Immediately downstream of each of the nine putative sRNAs is a helix-turn-helix DNA binding protein (termed Trp1-9 for Transcriptional Regulatory Protein 1-9) that is poorly transcribed as determined by RNA-Seq. This gene organization is suggestive of a potential cis-acting RNA mechanism or riboswitch with the RNA secondary structure controlling transcription of the cognate downstream trp.