The South Eastern Arabian Sea (SEAS) margin represents a tropical eastern boundary upwelling system, which is subjected to intense seasonal hypoxia in the continental shelf, and impingement of oxygen minimum zone (OMZ) along the continental slope. This paper provides the first comprehensive information on abundance, diversity and distribution patterns of echinoderms, which are highly sensitive to oxygen deficiency and anthropogenic disturbances, in the continental shelf (∼20–250 m) of the SEAS. Results are based on depth stratified and seasonally resolved sampling at 241 sites, representing 8 latitudinal grids & 4 depth strata (from inner shelf to shelf edge) using naturalist dredge and Smith-McIntyre grab. Echinoderms were the numerically dominant group among epifauna (42%), with significant seasonal variations in relative abundance (71% during winter and 17% during summer monsoon). Fifty-five species of echinoderms were identified, among which ophiuroids showed highest diversity (24 species) followed by echinoids (11 species) and asteroids (8 species). Species richness of echinoderms was higher in the inner and mid shelf (20–80 m), while the group was nearly absent in the shelf edge (150–250 m). A significant negative correlation was noted between species richness and latitude, and three distinct sub-regions could be delineated based on species diversity and abundance. The observed distribution patterns were found to be determined chiefly by sediment texture and bottom water dissolved oxygen, along with anthropogenic disturbances (bottom trawling). Echinoderms showed maximum abundance and species richness in the well-oxygenated sandy sediments of the southern SEAS, and very low species richness and abundance in relatively silty sediments of the northern SEAS, which were characterized by high seasonal fluctuations in dissolved oxygen (seasonal hypoxia). The near absence of echinoderms in the shelf edge despite the availability of sandy substrates indicates that this group is more sensitive to the perennially low oxygen conditions prevailing here.