Abstract Seasonal observation on physico-chemical parameters were correlated with population of ostracoda in southern region off Rameswaram, Gulf of Mannar, Ramanathapuram district, Tamil Nadu, southeast coast of India, by collecting bottom sediment and water samples in the inner shelf region. 11 samples were collected every season, for four different seasons, namely, northeast monsoon (October 2010), winter (January 2011), summer (April 2011) and southwest monsoon (July 2011) seasons. Spatial and seasonal variation in physico-chemical and hydrographic parameters and sampling stations having higher population of ostracoda were critically analysed with the observed parameters. Highest population of ostracoda was recorded during summer followed by southwest monsoon, northeast monsoon and winter season. Cluster analysis reveal that station 9 falls in all seasons under favourable location, during different seasons and is having the most congenial environment for ostracoda to thrive. Depth, pH, dissolved oxygen, salinity, EC, TDS, nitrite and silica show positive correlation, and turbidity, nitrate and phosphate show negative correlation with total population of ostracoda.