Aedes aegypti mosquito species is a primary vector for dengue, chikungunya and Zika infections, and vector control is the only key approach for reducing their transmission. The present study emphasizes on environmental friendly approach for the fabrication of zinc oxide nanorods (ZnO NRs) using aqueous extract of Lumnitzera racemosa flower buds (LB) as a reducing and stabilizing agent. ZnO NRs were examined by UV-Vis spectroscopy with characteristic absorbance band at 373.82 nm and bandgap of 3.25 eV. FT-IR analysis revealed the functional groups associated with ZnO NRs. The crystallinity of LB-ZnO NRs was further investigated using X-ray diffraction. The Zeta potential displayed a surface charge of − 23.5 mV on NRs. Energy dispersive spectra analysis and SEM analysis confirmed the formation of ZnO NRs whilst TEM highlighted the average length and diameter in the range of 250-300 nm and 45-50 nm respectively. LB-ZnO NRs were found to be efficacious against Ae. aegypti 4th instar larvae with LC 50 of 24.74 μg/ml. Decreased acetylcholinesterase (60.6%) and glutathione S-transferase (24.4%) activities were also evaluated in Ae. aegypti larvae which were exposed to synthesized LB-ZnO NRs with no genetic aberrations. All these outcomes propose the potential employment of LB-ZnO NRs in mosquito control, as well as an effective alternative to insecticide resistance.