In the present research of isolation, identification and physicochemical parameters of two different marine water sample of Jamboranodai and Thondiyamkadu village from Thiruvarur district. The isolation of cyanobacteria like Arthrospira jenneri, Aphanocapsa koordersi, A. platensis, Gloeocapsa crepidium, G. gelatinosa, G. livida, G. punctata, G. samoensis, G. sanguine, Hyella caespitose, Oscillatoria acuminate, O. amoena, O. homogenea, O. laetevirens, O. minimus, O. pseudogeminata, O. schultzii, O. subbrevis, O. trichoides, Spirulina laxissima, S. meneghiniana and S. subtilissima were recorded from two different places in Thiruvarur district and identified on the basis of characters was also observed. Among the two different places, the Jamboranodai village has maximum number of colonies (119) and Thondiyamkadu village has minimum at (75) were recorded. The water physicochemical properties such as temperature, pH, organic carbon, organic matter, dissolved oxygen, BOD, COD, salinity, available nitrogen, phosphorus, potassium, zinc, copper, iron, manganese and sodium, calcium, magnesium, potassium. The maximum parameters in Thondiyamkadu village were (34ËšC), (8.0pH), (0.74%), (0.82%), (288.26mg/kg), (47.61mg/kg), (318.17mg/kg), (0.89ppm), (0.70ppm), (6.75ppm), (3.43ppm), (3.1ml/L), (3.5ml/L), (1.9ml/L), (34%), (1.86ppm), (1.71ppm), (1.83ppm) and (0.97ppm) when compared to Jamboranodai village was recorded. The Shannon (H) and Simpson (D) diversity indexes were calculated respectively. Cyanobacteria are important for optimizing the growth of many plants when used as biofertilizers.