Selenium is an important micronutrient which is essential for the normal functioning of cells and tissues. The efficacy and bioavailability of selenium significantly improves in the nano form of selenium. In the present work, Selenium Nanoparticles (SeNPs) were synthesized from aqueous extract of lemon juice. The synthesized SeNPs were characterized by Scanning electron microscopy, X-Ray diffraction, FT-IR and Zeta potential analysis. SEM analysis exhibited an uniform distribution of smooth surfaced spherical SeNPs. UV analysis and FT-IR analysis confirmed the presence of various functional groups present in the nanosuspension. X-Ray diffraction studies revealed the amorphous nature of the synthesized nanoparticle. The results of Zeta potential results implied very high stability of synthesized SeNPs. The SeNPs (1-3 µg/ml) were further subjected to toxicity analysis using 24 hours post fertilized (hpf) zebrafish embryos. Developmental stages of the embryos from 24 hpf to juvenile stage were noted. The survivability of embryos was 100% in 1 µg/ml concentration of SeNPs, 89% in 2 µg/ml and 81% in 3µg/ml concentration of SeNPs and compared with control. The survival rate, heartbeat rate, hatching rate of SeNPs treated zebrafish embryos right from 24 hpf to juvenile stage is noted and compared with untreated embryos and found to be higher in SeNPs treated embryos. Antioxidant activity of the prepared SeNPs was also higher and there was a dose dependant increase in activity was seen which is attributed to the presence of flavonoids and alkaloids present in the lemon extract capped SeNPs. The results strongly suggest that SeNPs could improve the production of quality of fingerlings in all aquaculture species.