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Little is known about the survival and effect of rapid climate warming on Pseudoalteromonas in the Arctic, although it is abundant and important in this ecosystem. Here, we investigated a cold-adapted Pseudoalteromonas fuliginea BSW20308 from the Arctic Ocean, from the genome to its transcriptomic responses towards temperature changes. It contained two circular chromosomes, with the second chromosome probably evolved from an ancestral plasmid. The evolution of multipartite genomes may be advantageous for its survival under changing environments. RNA-seq analysis revealed the extensive involvement of sRNome in response to temperature stress for the first time, especially tmRNA and a novel Pf1 sRNA strongly induced under heat stress. The present study makes significant contributions towards the understanding of Pseudoalteromonas in two aspects: the genome structure and evolution of its two chromosomes, and the important discovery of the sRNome in response to temperature stress.