Increased fisheries products have raised by-products that are discarded due to low economic value. In addition, marine by-products are still rich in protein and nutritional value that have biological activities and give benefits to human health. Meanwhile, there is raised pressure for sustainability practices in marine industries to reduce waste and minimize the detrimental effect on the environment. Thus, valorization by-products through bioactive peptide mining are crucial. This review focus on various ways to obtain bioactive peptides from marine by-products through protein hydrolysis, for instance chemical hydrolysis (acid and based), biochemical hydrolysis (autolysis and enzymatic hydrolysis), microbial fermentation, and subcritical water hydrolysis. Nevertheless, these processes have benefits and drawbacks which need to be considered. This review also addresses various biological activities that are favorable in pharmaceutical industries, including antioxidant, antihypertensive, anticancer, anti-obesity, and other beneficial bioactivities. In addition, some potential marine resources of Indonesia for the marine biopeptide from their by-product or undesired marine commodities would be addressed as well.