Fungicides play a crucial role in modern agriculture by effectively managing fungal diseases that can severely impact crop yield and quality. Hexaconazole, a widely used fungicide, has been proven effective against various fungal pathogens, making it an essential tool for crop protection and disease management strategies. Understanding the effects of Hexaconazole on plant physiology, particularly root growth and stomatal characteristics, is crucial for optimizing its application and ensuring sustainable agricultural practices growth. Therefore, his study aimed to investigate the effects of Hexaconazole (HEX), a fungicide, on root growth and stomatal characteristics of Allium cepa L. Different concentrations of Hexaconazole (0.0 as control treatment with only distilled water, 0.5, 1, and 1.5 ml/L) were utilized. The parameters examined included root length, root percentage, number of roots, and germination percentage. Additionally, stomatal features such as stomata number per mm², stomata length (µm), stomata width (µm), stomata index, and number of epidermal cells per mm² of the abaxial surface of the tubular leaf were analyzed. The results revealed that the control group exhibited the highest root length (7.11 cm), followed by T1 (4.27 cm), while the other treatments (T2 and T3) displayed significantly lower values (3.44 cm and 2.83 cm, respectively). In terms of root number, the T3 group recorded the highest number (67.75), whereas the control group exhibited the lowest root number (38.25). A highly significant correlation coefficient was observed between the number of roots and the root percentage. Regarding stomatal features, Allium cepa L. exhibited similar internal structural characteristics, but variations were observed in the measurements of stomatal traits. In general, the findings of this study contribute to the understanding of the impact of hexaconazole on root growth and stomatal characteristics in Allium cepa L. However, further research is warranted to elucidate the underlying mechanisms and potential implications of these findings.