Nanoparticles are particles with sizes between 1 and 100 nanometers (nm). Owing to their unique chemical, electrical, mechanical, optical, and piezoelectric properties, zinc oxide nanoparticles (ZnO-NPs) are finding widespread use in numerous applications with yearly production over 550 tons per year. Increasing use of ZnO NPs, and NPs in wastewater discharges from domestic and industrial sources will have significant potential for adverse impacts on aquatic phototrophic organisms. Comparative studies on microalgae species response to ZnO NPs and variation in tolerance among species is still mostly unexplored. The proposed research aims to evaluate interspecies’ variation in tolerance to ZnO NPs among marine and freshwater microalgae. Multi-well culture plate and flask culture screening methods were utilized for assessing microalgae species’ tolerance to various levels of ZnO NPs. Microalgae cell morphology changes in response to nano ZnO exposure were explored using both the Optical Coherence Microscope (OCM) and SEM. Availability of Nano ZnO tolerant microalgae species may provide an impetus for future studies to understand the mechanism of tolerance and potential applications in NPs bioremediation in aquatic systems.