In the present investigation suggested that the qualitative bioactive compounds analysis from microalgae stigonema sp and spirullina sp with methanol and hexane were individually estimated. The bioactive compounds like Alkaloids, Anthraquinone, Amino acid, Carbohydrate, Flavonoids, Phenols, Protein, Steroids, Saponin, Tannin and Terpenoids were qualitatively analysed from stigonema sp. whereas spirulina sp. was Alkaloids, Amino acid, Carbohydrate, Steroids, Saponin, Tannin and Terpenoids presented in methanolic extract but anthraquinone flavonoids and saponins were absent. The quantitative bioactive compounds like alkaloids aminoacid, carbohydrate, flavonoids, protein steroids, tannin and terpenoids were represented in methanolic and hexane solvent. The methanolic extract of stigonema sp. and spirulina sp. were individually maximum produced when compared with hexane solvent. The screening of microalgae by the effect of antibacterial properties of stigonema sp with different concentration of 25, 50, 75 and 100 µl extract were treated with Bacillus cereus, Klebsiella pnemoniae, proteus vulgaris, Pseudomonas aeroginosa and Staphylococcus aureus bacteria and 100 µl concentration of stigonema sp. was excellent zone inhibition observed. Whereas hexane extract also moderate zone of inhibition were performed with respective clinical bacteria. The effective antibacterial activity of spirulina sp higher concentration of methanolic extract was minimum zone of inhibition against some clinical bacteria respectively. The evaluation of antifungal activity of stigonema sp. and spirulina sp with methanol and hexane solvent were performed. The microalgae stigonema sp. was extraordinary antifungal activity than stigonema sp.