Although Shewanella putrefaciens is the specific spoilage organism in most seafood, only seven Shewanella phages have been sequenced and their endolysins have not been reported until now. In this study, we cloned and expressed two lysis-related proteins (Spp64 and Spp62) encoded by phage Spp001, the first sequenced S. putrefaciens phage. Both recombinant proteins showed strong lytic capability toward chilled S. putrefaciens Sp225 and presented a wider activity spectrum compared with bacteriophage Spp001. The enzymatic activity of crude Spp64, Spp62ΔTD, and Spp62ΔTD-GST can cause decreases of 0.691, 0.674, and 0.685, respectively, as tested through the turbidity reduction assay. Furthermore, purified enzyme Spp64 at concentrations of 537.5 and 4.20 μg/mL was enough to decrease the optical density of chilled S. putrefaciens by 0.881 and 0.492, respectively, within 15 min. The recombinant Spp64 has a peptidase catalytic domain and exhibits high temperature resistance. Moreover, Spp64 displayed superior enzymatic activity in a range of pH values that matches environmental conditions (pH between 5.0 and 10.0), which demonstrates that its application in seafood is feasible. The present work is to our knowledge the first report on lysis-related enzymes encoded in the Shewanella phage. Both proteins presented extraordinary potential to control S. putrefaciens; we hope that these proteins can be developed as novel antibacterial agents in further research.