Asteroids have been shown to produce a wide diversity of unique secondary metabolites, including a variety of saponins. Saponins are recognised as defensive compounds yet have also shown bioactivities that may be applied as pharmaceuticals, including anti-cancer. This PhD research has utilized the Australian native Crown-of-Thorns Starfish to evaluate existing saponin purification and identification methodologies. This initially required the development of a marine saponin database, followed by a comprehensive optimisation of saponin purification from tissues, using liquid-liquid separation and cartridge-based methods. Subsequently, the optimised procedure was used to characterise saponins released by CoTS into the surrounding water, which are likely necessary for defence or conspecific communication. These findings have implications in the purification of asteroid-derived saponins that may be applied to human health, as well as opens the door towards utilising saponins as a diagnostic tool for the rapid identification of CoTS in the wild.