Protein plays an important role in deterioration of fish and shrimp during preservation. An experiment was conducted to evaluate the protein degradation in muscle tissue of three shrimp species Penaeus monodon, Penaeus indicus, Metapenaeus dobsoni and fish Upeneus vittatus. Amount of protein estimated at weekly intervals of 49 days. The results of the present study were revealed that the maximum percentage degradation of insoluble proteins of 72.82% was recorded in P. indicus, whereas minimum percentage of insoluble proteins of 57.1% was reported in M. dobsoni after 49 days of preservation. Similarly with reference to degradation of soluble proteins the maximum percentage of 62.9% was reported in U. vittatus and minimum of 60% was recorded in P. monodon after 49 days of preservation.