In this work we analyzed changes in gene espression in Shewanella baltica upon cold stress. In order to imitate natural environment, we cultured bacteria in the Instant Ocean medium in a chemostat. Samples were collected after 90 and 180 minutes of cold stress and analyzed by RNA sequencing. The transcriptomic response could be characterized as global downregulation of gene expression (613 genes downregulated) and we found only 242 genes which were upregulated. We randomly tested 11 transcripts with RT-qPCR to confirm changes observed in RNA seq experiment. We observed change in expression of sigma factors namely, downregulation of the housekeeping sigma 70 encoded by rpoD and upregulation of ECF subfamily RNA polymerase sigma 24 factor rpoE2, indicating global transcription reprogramming. Analysis of metabolic pathways revealed common changes observed in other bacteria such as change in fatty acid metabolism toward synthesis of unsaturated fatty acids and upregulation of flagellar assembly genes after 90 minutes of cold stress. A novel observation was downregulation of genes encoding components of the type II secretion system. In summary, Overall design: Bacteria were cultured in Instant Ocean medium in a chemostat, at 20C and cold stress was induced by shifting to 8C. Experiment composed of five samples: single control sample (before stress) and samples collected after 90 and 180 minutes (in duplicates).