Marine capture fisheries contribute over 50% of total world fish production and more than 70% of this production is utilized for processing. The Canadian commercial fishing industry is one of the world’s most valued industries but generates large quantities of solid waste and wastewater. The increasing growth of the fish processing industry, the need for reduction of pollutants and the need to increase returns on raw material has led fish processors to adopt new ways of utilizing the wastes. In particular, efforts have focused on converting the biological substance in solid fish processing waste to various valuable compounds including both nutritional and non-nutritional products. Sulfated glycosaminoglycans (sGAGs) are heteropolysaccharide molecules with potential therapeutic applications and anticoagulant properties. Anticoagulants are responsible for curing major death-causing diseases such as strokes and cardiovascular diseases. The aim of this study was to develop an economically feasible technique to extract sulfated glycosaminoglycans (sGAGs) from fish processing waste. Two different fish (mackerel and herring) were used to optimize the extraction of sGAG. The effects of hydrolysis time (3, 6, 12 and 24 hrs) and papain concentration (15 and 20u/ml) on the extraction of sGAGs from different fish parts (whole fish, flesh, head, gut, fins and tails, skin and bones) were evaluated. The highest concentration of sGAGs (206.7 mg/g) was obtained from the mackerel head sample at 6 hrs of hydrolysis time and 20 u/ml of enzyme concentration while the highest concentration of sGAGs (236.3 mg/g) was obtained from herring gut at 12 hrs of hydrolysis time and 20 u/ml of enzyme concentration. The concentration of sGAG obtained from other part of mackerel were flesh (23.96 mg/g), waste (163.23 mg/g), fins and tail (86.63 mg/g), gut (203.52 mg/g), skin (105.45 mg/g) and bones (97.2 mg/g). However, the concentration of sGAG obtained from other parts of herring were flesh (39.34 mg/g), waste (130.15 mg/g), head (162.76 mg/g), fins and tail (148.53 mg/g), skin (65.89 mg/g) and bones (75.57 mg/g). Comparing the overall concentration of sGAG in waste samples of the fish, the mackerel produced higher sGAG than the herring.