Abstract: The present study aimed to establish the information on protozoan diseases in Black tiger shrimp Penaeus monodon during the year 2012. Due to high levels of ciliate infestations can affect respiration, feeding, growth, survival and also irritation behaviour of larvae (zoea, mysis and post larvae) was observed. Protozoan diseases in P. monodon was global problem in hatcheries mainly affect the eggs and larval stages. In current study we found different variations of ciliary infections were observed throughout the year (2012), we also concentrated on some physical parameters like PH, Temperature ( to C), and salinity (ppt), variations of these parameters will affect the larval growth and survival rate in hatchery system.