The growth as well as morphological and physiological features of thermophilic cyanobacteria vary greatly depending upon the physico-chemical factors prevailing in the water of hot springs. Effects of some physico-chemical parameters of water like-temperature, pH, nitrate and phosphate contents were observed on a thermophilic cyanobacterium Fischerella thermalis isolated from a hot water spring located at Panifala, Burdwan, West Bengal. Catalase activity under varying temperatures and light intensities was also studied in in vitro condition. Filaments incubated at 45 o -55 o C temperature, acidic (5.0-7.0) and highly alkaline (10.0) pH, high concentration (1.0-2.0 g/L) of NaNO 3 and low (0-0.02 g/L) as well as high concentration (0.1 g/L) of K 2 HPO 4 showed various morphological abnormalities like shrinkage of cells, degradation of cellular contents, twisted and broken trichomes, discolouration of filaments, empty filaments. Such variations in physical and chemical factors also resulted in variations in protein, carbohydrate, chlorphyll-a and carotenoid contents. Heterocyst frequency and branching frequency was highest at 37 o C temperature, 8.0-9.0 pH and 0.06 g/L of K 2 HPO 4 concentration. At increasingly high concentration of NaNO 3 branching frequency increased but heterocyst frequency decreased. 37 o C temperature, pH 8.0, 1.0 g/L NaNO 3 and 0.06 g/L of K 2 HPO 4 concentration were found to be ideal for growth in in vitro condition. High light intensity (75 photons m -2 s -1 ) and low temperature (25 o C) were observed to be responsible for increased catalase activity. This investigation will help to optimize the culture medium for in vitro production of biologically significant organisms like filamentous thermophilic cyanobacteria and throw light on experimental taxonomy.