Thraustochytrids, aplanochytrids and labyrinthulids belong to the Class Labyrinthulomycetes of the Kingdom Straminipila or Chromista, which also includes diatoms, brown algae, oomycetan fungi and a variety of photosynthetic and non-photosynthetic flagellates. The Labyrinthulomycetes are emerging to be an important group in the marine food web dynamics. Yet, their role in the marine environment has been poorly elucidated. They have been widely studied in coastal environment but little is known about their abundance and distribution in the oceanic environment. The four major objectives of the present study were: 1. To isolate thraustochytrids and aplanochytrids from zooplankton in oceanic waters, to characterize them with respect to their life cycle in order to identify them and to group them based on their carbon and nitrogen nutrition and production of extracellular enzymes. 2. To study the abundance of thraustochytrids and bacteria in oceanic water column to understand their relations. 3. To carry out molecular characterization of isolates obtained from zooplankton based on their 18S ribosomal RNA gene and ITS sequences 4. To design molecular probes for a few isolates to enable their detection in natural samples.