Regular fortnightly zooplankton sample collection was made for two years from November 1993 to October 1995 in the Palk Bay (Station I) and Gulf of Mannar (Station 11 & III) along the south east coast of India. Among the zooplankton sample particularly protozoa diversity were identified. Their primary peak was observed at the middle of summer (Station I) and pre-monsoon (Station I1 and 111) months. The temperature and salinity and monsoonal factors mostly influenced the occurrence of protozoans, the results are interpreted and probable reasons discussed.