Along with the development and innovations in genetic engineering and biotechnology, aquaculture breeding has expanded from traditional selective breeding and hybrid breeding to marker- assisted selective breeding, cell engineering breeding, genome-wide genotyping-based selective breeding, molecular design breeding, sex control breeding, gene transfer, gene editing, and other molecular marker-assisted breeding technologies. Although the aquaculture seed industry has advanced, several problems and challenges remain such as the low coverage rate of improved varieties and insufficient research depth. This review provides a detailed analysis of the main advances made in the field of aquaculture technology and summarizes the commercially valuable germplasm resources of echinoderms (sea cucumbers and sea urchins) and their applications. We also propose to the sea cucumber and sea urchin breeding industry to provide a reference for the development of germplasm resources for echinoderms of commercial value and promote the green development of the aquaculture industry.