There are several toxic microalgae species known as Harmful algal bloom (HAB) causing serious effects to the environment and economy. Knowledge on these groups of marine micro-flora is scanty and several areas remain unexplored. The present study focuses on the analysis of microalgal diversity in the Malabar coastal areas at Southwest and Northeast monsoon. The diatoms, dinoflagellates and total microalgal population were analysed and quantified. Predominant species were identified. Physicochemical parameters of the seawater at different time intervals and Correlation between diatoms, dinoflagellates and total microalgae population with physicochemical parameters were identified. From the analysis, a total of 53 diatoms and 15 dinoflagellates were identified. The predominant species including toxic or harmful bloom-forming were found to be Dinophysis caudata, Noctiluca scintillans, Prorocentrum lima and Tripos furca. The total microalgae population varied from 18,592 cells/L to 7,832 cells/L in the months of April and December. Dinoflagellates were positively correlated with salinity (r = 0.848; p = 0.008), nitrite (r = 0.752; p = 0.032) and total phosphorous (r = 0.734, p = 0.038). Diatoms were positively correlated with temperature (r = 0.804; p = 0.016) and nitrate (r = 0.774, p = 0.024). Total microalgal density was positively correlated with temperature (r = 0.825; p = 0.012) and nitrate content (r = 0.811, p = 0.15).