As a free living diazotrophic prokaryotic microorganism, Cyanobacteria produce a wide array of toxic chemicals and secondary or bioactive metabolites. Allelopathic interactions involving Cyanobacterial flora are being explored for their pharmaceutical and environmental significance. Cyanobacterial allelopathy can be regarded as one of the significant factors influencing their dominance in diverse habitats and as unique producers of a variety of allelochemicals that can be utilized as eco-friendly bio-control agents. In present work detrimental effects of locally isolated Cyanobacterial strains were evaluated against plant pathogenic three fungal isolates (Fusarium oxysporum, Sclerotium rolfsi and Rhizoctonia solani). It was observed that the crude extracts of four Cyanobacterial isolates (Microcystis aeruginosa, Oscilatoria princeps, Anabaena anomala and Nostoc calcicola), were capable of diminishing the growth and further development of phyto-pathogenic fungal isolates. Whereas M. aeruginosa showed more antifungal activity compared to other cyanobacterial strains and its Methanol extracts were observed more efficient against local fungal isolates Fusarium oxysporum (% MI ? 88.46 ? 0.24) and Sclerotium rolfsii (83.42) as compared to Rhizoctonia solani (78.33). Toxic as well as allelopathic potentialities of cyanobacteria have needed to be further investigation that can offer promising solutions to bio-control against pathogenic microorganisms, providing novel bio-fungicides.