Chaetoceros calcitrans is a small, fast-growing marine diatom used widely in aquaculture industries, as it is comprised of high nutritional value essential for most of the marine filter feeders. It is rich in EPA and Vitamins (B2 & C). It is often used in hatcheries, particularly in the production of shrimp larvae and bivalve spat. This species gives vital energy and organic nutrients for the growth and development of larvae and juveniles. Based on the importance of Chaetoceros calcitrans culture, an attempt was tried to harvest the microalgae biomass by flocculation. Flocculation of the Chaetoceros culture was performed in 500ml beaker with the adjustment of pH with 5N NaOH. The pH varied from 8.4 - 11.9. Flocculation efficiency was estimated at 4hrs from an aliquot of the medium which was collected for measuring optical density from a height of 100cm from the bottom of the beaker. The optical density of the aliquot was measured by UV spectrophotometer (Biotech Epoch 2) at a wave length of 750nm. Structural stability of the flocculated micro algal concentrate was investigated by Evans Blue staining. The flocculation efficiency showed significant (p<0.05) increase from initial pH of 8.4 to the induced pH of upto 10.2 and it was reduced at pH of 10.3 and henceforth became stationary upto pH of 11.9. The Evans Blue staining confirmed that the cells were individually dispersed upto induced pH of 10.2. It was observed not to take any stain so that the microalgal cells were intact with good viability so that the culture is able to progress from the flocculated cells. Whereas, for the cells flocculated with induced pH of 10.3 to 11.9, the cells were aggregated and the Evan's blue solution was diffused into their protoplasm region and stained the cells blue in colour. So it is concluded that induced pH of 10.2 may be optimum with better flocculation efficiency for the harvesting of Chaetoceros calcitrans.