The present study is conducted to evaluate the biological control aptitude of the two cyanobacteria (blue-green algal) i. e., Anabeana variabilis and Nostoc paludosum, cultural filtrates against the causal of fennel damping-off and root-rot diseases i.e., Fusarium solani, Macrophomina phaseolina and Pythium aphanidermatum in vitro and in vivo. Culture filtrate of both blue-green algal had antifungal effect against the growth of the three pathogenic fungi. Under artificial inoculation conditions in a greenhouse experiment, both algae were found to be effective against fennel damping-off and root-rot diseases compared with untreated control. N. paludosum culture filtrate was the most effective than A. variabilis in reducing damping off and root-rot diseases as well as increased activity of hydrolytic enzymes included peroxidase, polyphenoloxidase, chitinase as well as oil content, soluble proteins and total phenols of fennel plants. Under natural field conditions during 2020/ 2021 and 2021/ 2022 seasons, both algal had biocidal effect against the fennel soil-borne diseases and significantly increased growth parameters and plant yield. It was observed that both blue-green algal filtrates increased volatile oil percentage and its frequency compared with untreated seeds.