The spatial and seasonal patterns of distribution of Cyanobacterial species and their abundance in relation to physicochemical parameters were studied from April, 2002 to March, 2003 in two stations of Uppanar estuary in the south-east coast of India (Lat. 11°42’N: Long. 79°49’E). As many as 15 Cyanobacteria species were recorded from different family viz. Chroococcaceae (4), Oscillatoriaceae (7) and Nostocaceae (4). The concentration of nutrients was low during summer season and more number of Cyanobacteria was recorded in monsoon season