Stichopus hermanni and Stichopus vastus are sea cucumber species from the Stichopodidae family within the coastal waters of Malaysia. The integument of these invertebrates is hypothesised to contain abundant glycosaminoglycans (GAGs). GAGs are divided into non-sulphated and sulphated GAGs. Sulphated GAGs have various chemico-biological functions that are beneficial to humans. This study quantitatively analysed N-, O-sulphated and total sulphated GAG content from three different anatomical regions (integument, internal organs and coelomic fluid) of S. hermanni and S. vastus. The integument revealed the highest content of total, O- and N-sulphated GAGs, followed by the internal organs and the coelomic fluid for both species of sea cucumbers. The percentage division of O- and N-sulphated GAGs suggested that anatomical parts of both species showed higher levels of O-sulphated GAGs compared to N-sulphated GAGs. In conclusion, these findings indicate that the integument body wall of S. hermanni and S. vastus is a rich source of sulphated GAGs.