Fungal metabolites are considered to be most efficient tools to overcome the issues related to insecticide resistance and environmental pollution. The present study focus on the evaluation of the mosquito larvicidal efficacy of metabolites of seven indigenous fungal isolates (Penicillium sp. Aspergillus niger, A. flavus, A. parasiticus, Rhizopus sp. Mucor sp. and Aspergillus sp.) on the larvae of Aedes aegypti and Culex quinquefasciatus under the laboratory condition. The preliminary screening of the isolate, Penicillium sp. showed better larvicidal effect when compared to other fungi. The fungus was grown on Potato Dextrose Broth (PDB) in the laboratory (at 25°C) and maintained in the relative humidity (at 76 ± 4% for 15 days). Larvicidal potency of mycelial ethyl acetate extract (MEAE) of Penicillium sp. was performed against 1st to 4th instars larvae of Ae. aegypti and Cx. quinquefasciatus using four different concentrations (100, 200, 300, and 500 μg/ml) that showed better larval mortality values (μg/ml) of LC50 = 6.554, 5.487, 6.874, 6.892, and the LC90 = 11.486, 10.366, 12.879, 13.865 for Ae. aegypti and LC50 = 7.000, 13.943, 18.129, 25.212 and the LC90 = 12.541, 23.761, 30.923, 41.696 for Cx. quinquefasciatus. Exposure of metabolite to larvae resulted in behavior changes i.e., excitation, up and down with aggressive movement, anal papillae biting behavior. Further, the larvae treated with Penicillium sp. metabolite exhibited significant reduction in the levels of acetylcholinesterase. The 4th instar mosquito larvae treated with the 500 μg/ml mycelia extract showed severe histological damages. During the antibacterial analysis of Penicillium sp.- mycelium the maximum growth inhibition zone was recorded in Shigella dysenteriae (31.2 mm) and Klebsiella pneumoniae (31.1 mm) followed by others. In addition, to check the toxicity of Penicillium sp. MEAE against embryos of Zebrafish, a model system, using different concentrations of metabolites (1.0, 0.5, 0.125 mg/ml, 30, 3.0, and 0.5 μg/ml) and life-stage parameters were observed at 124 hpf. Furthermore, the Fourier Transformed Infrared and GCMS spectrum analysis of mycelium reflected several chemical compounds. The outcome of the study clearly shows that Penicillium sp. metabolites could serve as an ideal eco-friendly, single-step and inexpensive source for the control of Ae. aegypti and Cx. quinquefasciatus larvae.