A study of radiolarian fluxes collected during 1991-93 from time-series sediment traps deployed at 1071 and 3010 m water depth in the southern Bay of Bengal (SBBT) yielded 40 species/groups of radiolarians. Among the order Polycystina, the species of sub-order Spumellaria were by far the most abundant (approx. 95%) followed by sub-order Nassellaria (5%). This is contrary to reports from the Atlantic and Pacific Oceans and is attributed to the prevailing hyposaline condition resulting from the monsoonal rainfall. Higher radiolarian fluxes occurred during March-May, when moderate salinity and a high sea surface temperature (SST) regime prevailed at the trap site. R-mode cluster analysis of the radiolarian flux data revealed three assemblages represented by the cooler (1) and warmer (2) surface dwelling fauna (0-50 m) dominated by spumellarians, and a deeper dwelling (3) sub-surface fauna (50-100 m) associated with deep dwelling (more than 100 m) nassellarian species. Spongaster tetras tetras, a surface water radiolarian species, exhibited its preference for high SST and moderate salinity conditions during the pre-monsoon season (March-May). Radiolarian fluxes responded to seasonal changes in SST and salinity variations due to the monsoonal precipitation, and the freshwater runoff from the Indian rivers causing a hyposaline condition in the Bay of Bengal. Results imply that the radiolarian assemblages in the down core data may reveal the monsoonal history in the geological past.