Nanobiotechnology has developed as an effective technology for developing antimicrobial nanoparticles in an environmentally safe manner. In this study, green synthesized zinc oxide nanoparticles (ZnO NPS) from zinc acetate solution by using lemon peels aqueous extract was characterized by UV–Visible Spectroscopy, High-resolution Transmission Electron Microscopy (HR-TEM) and Dynamic Light Scattering (DLS). Anticandidal activity was investigated against three clinical multidrug resistant Candida species including two Candida albicans, one Candida glabrata and one Candida krusei using four antifungal agents by disc diffusion method and antifungal activity of ZnO NPS was assayed by disc diffusion method and determination of the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC). Characterization studies revealed that the synthesized nanoparticles have rod shape with sizes of 13.58 - 30.70 nm. Notably, high rates of resistance were observed with the four tested antifungal agents against all Candida species and the antifungal activity of the synthesized ZnO NPS against Candida species were exhibited, with a maximum zone of inhibition of 24.5±0.5 mm against C. glabrata followed by C. albicans (19.5±0.5 mm) and C. krusei (16.0±0.0 mm). MIC and MFC for all Candida species were 0.25 and 0.5 mg/ml respectively. The cytotoxic data indicates that ZnO NPs have half maximal inhibitory concentration (IC50) value = 230.12 ± 9.34 μg/ml on normal human lung fibroblast cell line (MRC5). In conclusion, the study elucidates that lemon peels mediated green synthesized zinc oxide nanoparticles have antifungal activity against different Candida species. So that it can be developed as a novel medicine for the treatment of Candida associated infections in the near future.