In the present study, the essential oil (EO) of Hyptis suaveolens has been explored for the first time for its phytotoxic and cytotoxic activities. The phytotoxic activity was assessed against rice (Oryza sativa) and its major troublesome weed, Echinochloa crus-galli, under laboratory and screenhouse conditions. GC-MS analysis revealed EO to be monoterpenoid (~ 79% monoterpenes) in nature with α-phellandrene (22.8%), α-pinene (10.1%) and limonene (8.5%) as the major chemical constituents. The laboratory bioassay showed a complete growth inhibitory effect of EO (≥ 2 mg mL-1) towards the germination and seedling growth of E. crus-galli. However, the inhibitory effect on rice was much less (~40% inhibition). EO caused visible injury, reduction in chlorophyll content, cell viability and ultimately led to complete wilting of E. crus-galli plants. In addition, EO altered the cell division in the meristematic cells of Allium cepa as depicted by ~63% decrease in mitotic index. EO exposure induced several aberrations at chromosomal (c-mitosis, anaphase bridges, chromosomal breakage, vagrant chromosomes, and sticky chromosomes) and cytological level (cytoplasm destruction, peripheral nuclei, and bi-nucleate cells). The present study concludes that H. suaveolens EO possesses phytotoxic activity due to its mito-depressive activity, and could serve as a natural herbicide under sustainable agricultural practices.