Monitoring and surveillance of algal blooms along the southwest coast of India, both from the coastal and estuarine stations were made during 2005-08. Algal blooms of Coscinodiscus asteromphalus var. centralis Ehrenberg were observed during the monsoon 2006 off Kodikkal (near Calicut; 110 28 43’ N lat., 750 36 10’E long.) and Coscinodiscus spp. and Pleurosigma spp. at Mahe estuary (110 42 18’N lat., 750 32 36’E). It is inferred that the high ratios of Si:N played a significant role in the formation of algal bloom. An attempt has been made to prepare a fingerprint of these blooms from the available biological and physico-chemical variables which would be helpful for predicting the algal blooms. During the study, eleven species of toxic microalgae were recorded indicating the possibility of potential threat of harmful blooms in the coastal waters of southwest coast of India.