• Using cyanobacteria extracts at low doses reduces the toxicity risk in cucumber seeds.• Optimal doses of cytokinins and salicylic acid benefit the early plant growth stages.• Cyanobacterial siderophores favor plant growth during the seedling phase.• Strain Nostoc SAB-M612 stood out for their stimulant ability in cucumber seedlings. This work clarifies some of the substances involved with the biostimulant effect shown by 28 cyanobacteria isolated from different aquatic environments. The production of salicylic acid, cytokinins, siderophores and phosphate solubilization were analyzed in vitro, as well as the phytostimulant/phytotoxic effect on watercress seeds at two different extract concentrations (0.5 and 0.2 mg mL−1). The most prominent plant growth promoting cyanobacteria were verified in vivo at two different doses (0.5 and 0.1 mg mL−1). 21.4 % and 7.1 % of the tested strains produced siderophores or phosphate solubilization, respectively. The production of salicylic acid was stood out for the strains Calothrix SAB-B797, Nostoc SAB-B1300 and Nostoc SAB-M612, while Nostoc SAB-M251 and Trichormus SAB-M304 were noticeable regard to cytokinin production. The highest values of germination occurred when the extracts were applied in low dose (0.5 mg mL−1). Nostoc SAB-M612 provoked the stimulation of aerial and radicular growth in cucumber seedlings.