Understanding the transect survey for abundance of anemone fishes and other living organisms is important to asses reef associated fish diversity in North Bay island. The percentage distribution of 10 different substratum from the disturbed, semi-disturbed and undisturbed areas was recorded during the survey in North Bay islands during November 2009 to April 2010. The survey observations reveal that the fishes were the dominant groups followed by mollusks, lobsters and octopus. There are 5 different anemone fishes were collected during the transect survey and their distribution is more in undisturbed area. We are standardizing the different mass culture techniques for production of phytoplankton and zooplankton for the nutritional source for the anemone fish larvae. Monitoring the water quality parameters and culture the phytoplankton and zooplankton used in different culture media with 2 adjustment studies like with and without salinity adjustment. The results of this experiment indicate that zooplankton was rich in protein and fat content and it will be used as high nutritional source for feeding fish larvae.