The invention discloses a method for sampling and extracting DNA from living echinoderms. The tube podia of living sea urchins or tube podia, tentacles or intestines of living sea cucumbers are taken, lysed and digested with a lysate added with DNase, and extracted and centrifuged to obtain the DNA. Supernatant, centrifugal removal of slag (bone flakes), ethanol precipitation, centrifugal separation, detection and other steps make the concentration and quality of the extracted DNA consistent with the DNA extracted from the traditional (dead body) sampling tissue of echinoderms. It is not necessary to kill echinoderms, but samples are taken from living organisms, and then DNA is extracted, so that molecular biology techniques can truly become an auxiliary tool for genetic breeding. Utilizing the invention, the echinoderm resources can be rationally utilized to carry out auxiliary breeding, breeding status monitoring, gene screening, family identification and the like. In addition, it is of great significance to the protection and research of many endangered species of echinoderms.