Cyanobacterial metabolites have gained a great attention during the last few decades, as they are a potential source for bioactive compounds. In the present study the total phenolic and flavonoid compounds in the biomass of Leptolyngbya sp. Q1 (MZ504747) and Desertifilum sp. Q2 (MZ504748) were estimated and their methanolic extracts were screened for their free radical scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and antimicrobial activity (well diffusion method) against different Gram-positive, Gram-negative bacteria in addition to Candida albicans. The results showed that Leptolyngbya sp. had higher total phenolic compounds content (8.89± 0.89 mg GAE/g DW) and total flavonoid content (1.72± 0.01 mg QE/g DW) compared to those recorded in Desertifilum sp. Both extracts were detected to have antioxidant activity against DPPH free radicals, and the IC50 values were 2.18 and 2.85 mg/ml for Leptolyngbya sp. and Desertifilum sp., respectively. Also, Leptolyngbya sp. extract was determined to have higher antimicrobial activity against tested microorganisms compared to Desertifilum sp. extract. Finally, the GC-MS profile for both extracts indicated the presence of phenolic compounds, saturated and unsaturated fatty acids such as 3-Allyl-2-methoxyphenol, Tetradecanoic acid (Myristic acid), n-Hexadecanoic acid (Palmitic acid), Phytol, Linoleic acid, Linolenic acid, Palmitoleic acid, cis-Vaccenic acid and other bioactive compounds of well-known pharmaceutical and industrial importance.