The present investigation suggests that the influence of metrological and Physico-chemical factors on the seasonal variation of cyanobacterial diversity were performed. Marine water samples were collected at monthly wise from Thondiyakadu coast for one year from July 2013 to June 2014 and Physico-chemical Parameters such as rainfall, atmosphere temperature, water temperature, pH, salinity, dissolved oxygen; Nitrate and total phosphorous were analyzed. Maximum rainfall was September may record during the period of 2013 to 2014. Maximum pH was June and July was recorded in the study. The results were discussed.