Echinoderms are a source of a broad range of secondary metabolites with a large variety of bioactive properties. Although pigment and lipid derivatives are the major groups of bioactive compounds found in crinoids and ophiuroids, saponins represent the most abundant and diverse marine natural products (MNPs) in the phylum Echinodermata. This review is for researchers that are interested in MNPs derived from echinoderms, but with a particular focus on the structural diversity and biological function of saponins. Among the echinoderms, these steroidal compounds are mostly known for and structurally most diverse within sea cucumbers. Through compilation of extensive tables, this review provides a reference book, summarizing not only the major chemical classes of well-known secondary metabolites in the phylum Echinodermata but also further focusing on the presence of bioactive saponins in echinoderms in general and within different sea cucumber species in particular. The final compilation aims to correlate the vast structural diversity of saponins with known biological functions. The here presented data revealed that holothurians, holotoxins, cucumariosides, and echinosids are not only the most abundant saponin compounds in various genera of sea cucumbers but that these saponins can also be used as potential chemotaxonomic markers for different sea cucumber species. By studying the structure-function relationships of triterpene glycosides in echinoderms in general, or in particular within holothurians, the vast structural diversity, taxonomic distribution, and bioactivity of the molecules can be deciphered, which provides an opportunity to focus future research efforts on target species that contain MNPs with novel pharmacological activities.