SummaryRapid softening of texture is a major problem associated with quality loss and consumer rejection of Harpiosquillid mantis shrimp (Harpiosquilla raphidea) (HMS). Effects of endogenous proteases in muscles and digestive tract on protein degradation and softening were investigated. Scanning electron microscopic and histological images indicated drastic destruction of muscle during iced storage. Based on autolysis, maximal activity was found at pH 8.5 and 55 °C and serine proteases including trypsin were dominant. Cathepsin B and L+B in muscle were altered throughout storage, while trypsin remained constant in HMS meat during 1‐3 days. Firmness and toughness decreased and coincided with augmented degradation of myofibrillar proteins and collagen. Trypsin from the digestive tract was contaminated into the abdomen during iced storage, therefore inducing drastic hydrolysis of muscle proteins, causing the undesirable pasty/mushy texture associated with the loss in firmness and toughness of meat within 3 days of storage.