Shewanella putrefaciens is a kind of specific spoilage organism of aquatic products， which possess strong cold adaptability and spoilage ability. Two-component signal transduction systems (TCSs) is one of the most important regulatory systems in bacteria， and plays an important role in the perception and response of bacteria to complex environment. In order to explore distribution and function of TCSs in S. putrefaciens. In this paper， the distribution， classification， structure and function of TCSs in S. putrefaciens from aquatic products， were systematically analyzed by bioinformatics methods， including whole genome identification， multiple sequence alignment， phylogenetic analysis， protein structural prediction and interaction protein analysis. The results showed that there were 31 histidine kinases (HKs)， 36 response regulators(RRs)， 3 pairs of TCSs and 3 fusion HKs in S. putrefaciens WS13. There are 16 types of structural domain compositions in HKs， 15 of which possess HATPase_c kinase catalytic domains. RRs have10 types of structural domain compositions， all of which contain REC domains. Multiple sequence alignment and evolutionary analysis showed that HKs and RRs with different structural domains had different evolutionary relationships， which suggested functional diversity of these proteins. The biological functions of 3 pairs of TCSs and 3 fusion HKs were predicted to be mainly involved in response to signal stimulation， regulation of various metabolic processes and transport of substances in cells. Moreover， 3 fusion HKs were related to the formation of trimethylamine. The results provide references for further exploring the function of TCSs in S.putrefaciens from aquatic products.