Three cyanobacterial filamentous, heterocystous isolates (A, B, and C) were isolated from sandy soil collected from the Ismailia Agricultural Research Station (ARC), Ismailia Governorate, Egypt. A polygenic approach was used to characterize these isolates, which included morphology, ultrastructure, and molecular analyses. The morphological analyses for the three strains agree with the molecular data (16S, ITS, and 23S rRNA sequences and phylogeny); the order of our isolates is: Nostocales and family: Nostocaceae, they identified as the following: isolate A: Trichormus variabilis; isolate C: Trichormus sp.) which are filamentous and terminal heterocysts; and isolate B: Nostoc sp.) colonies formed of filamentous heterocysts enclosed in a membrane and gelatinous polysaccharide sheath. Dry weight, pigment content, phytohormones, total nitrogen, total protein, exopolysaccharides, and phosphate dissolving were determined for three strains. The results showed that Trichormus variabilis has the highest chlorophyll a content, Nostoc sp. has the highest carotenoid content, and three strains have almost similar phycocyanin content, while three strains can secrete phytohormones and nitrogen in their medium and dissolve phosphate, with near values in Trichormus variabilis and Trichormus sp. and a slight difference in Nostoc sp. According to the findings of this study, cyanobacterial strains isolated from Ismailia Agricultural Research Station can be used as biofertilizers and nitrogen-fixing fertilizers because of their ability to secrete phytohormones and bioactive compounds and fix air nitrogen in free nitrogen medium.