Mosquitoes transmit serious human infections and cause a number of deaths in tropical and subtropical environment countries every year. In the present work the zinc-substituted hydroxyapatite Ca5−xZnx(PO4)3OH (x = 0, 0.05, 0.2 and 1.0) was synthesized by two different methods: the hydrothermal method and the sol–gel method. The phase formation, functional group and surface morphology of Zn-HAP were authenticated using X-ray diffraction, Fourier transform infrared and scanning electron microscopy-energy-dispersive X-ray spectroscopy, respectively. The antimicrobial activity of the synthesized compounds was tested against different organisms such as Escherichia coli, Staphylococcus aureus and Candida albicans. Moreover, excellent antimicrobial activity was observed for hydrothermal-synthesized (Zn-HAP) compound compared to that of the sol–gel method. The synthesized Zn-HAP nanoparticles were reported for larvicidal activity against the filarial and Japanese encephalitis vector, Culex quinquefasciatus. The hydrothermal-synthesized (1.0 M Zn-HAP) compound exhibited higher larvicidal activity (93 ± 6.62) with minimum lethal concentration LC50 (33.74 mg ml−1) (to kill 50% of the care for larvae of the relevant species) and LC90 (139.92 mg ml−1) (to kill 90% of the treated larvae of the respective species) after 24 h, respectively than that of the sol–gel method. © 2020, Indian Academy of Sciences.