The plankton radiolarian community was investigated in the spring season during the two-month cruise ‘Shiyan1’ (10 April–13 May 2014) in the Eastern Indian Ocean. This is the first comprehensive plankton tow study to be carried out from 44 sampling stations across the entire area (80.00°–96.10° E, 10.08° N–6.00° S) of the Eastern Indian Ocean. The plankton tow samples were collected from a vertical haul from a depth 200 m to the surface. During the cruise, conductivity–temperature–depth (CTD) measurements were taken of temperature, salinity and chlorophyll a from the surface to 200 m depth. Shannon–Wiener’s diversity index (H’) and the dominance index (Y) were used to analyze community structure. There was a total of 168 plankton species, composed of Acantharia, Phaeodaria, Polycystina, Collodaria and Taxopodida (monospecific—Sticholonche zanclea, Hertwig is the only recognized species). Hence, it included both celestine-based and siliceous organisms, which are also described here for the first time from this region. Total radiolarians ranged from 5 to 5500 ind/m−3, dominated by co-occurrences of Sphaerozoum punctatum and Stichonche zanclea species at the south-equator zone (SEQ)-transect 80° E and equator zone (EQ)-transect Lati-0. The possible environmental variables were tested through RDA analysis; although no result was obtained for the full species dataset, the samples from the equatorial transect related strongly to mixed-layer chlorophyll a concentration and those of a north–south transect to surface silicate concentrations or mixed-layer nitrate were significantly correlated (p < 0.01) to the radiolarian community. Our results indicate that the silicate and chlorophyll-a concentrations are the two major factors affecting the radiolarian distribution along two of the investigated transects (southern equator and equator) in the study area.