Microalgae are recognized for their exceptional versatility in producing bioactive compounds, as well as their capacity to generate high biomass, positioning them as ideal candidates for the large-scale production of various natural products with significant biotechnological potential. This study focuses on different microalgae species isolated from the Sids Agricultural Research Station (SARS) farm, located in Beni Suef Governorate, Egypt. The isolated microalgae were purified and molecularly identified as the green algae Desmodesmus abundans NA1 (D. abundans NA1), based on its 18S rDNA nucleotide sequence. Additionally, two blue-green algae species were identified as Nostoc paludosum NA2 (N. paludosum NA2) and Tildeniella torsiva NA3 (T. torsiva NA3) through 16S rRNA nucleotide sequence analysis. On bases of pigment production, D. abundans NA1was the pioneer, where chlorophyll (a) and carotenoid recorded their highest values at day eighteen of its growth curve (4.38 ± 0.14 & 1.14±0.023 µg/ml) respectively. All of the isolated microalga were found to produce growth hormones at considerable levels. While, N. paludosum NA2 and D. abundance NA1 were superior in producing an amazing value of cytokinins (782.8 ± 2.0 & 284.6 ± 1.0 mg/l) respectively. This study contributes to the knowledge on the potency of green and blue green algae to be used as a sustainable commercial producer of pigments and phyto- hormones on a large scale. These bioactive compounds could, in turn, be utilized in various applications, including biofertilizers,biofungicides, stress response regulators and fish feed. Further research is needed to explore the application of these microalgal isolates in field conditions, particularly under stress, to evaluate their ability to improve soil health, enhance plant resilience, and increase crop yields.