Abstract <p>In this study, the toxicity of methylchloroisothiazolinone/methylisothiazolinone (MCI/MI), a preservative widely used in cosmetics, personal care products, and various industrial applications, was evaluated using <i>Allium cepa</i> L. as a model organism. Physiological parameters included root length, weight gain, and germination percentage; cytogenetic parameters comprised mitotic index, micronucleus frequency, and chromosomal aberrations; anatomical parameters involved tissue damages; and biochemical parameters included superoxide dismutase and catalase activities, proline content, malondialdehyde levels, and chlorophyll <i>a</i> and <i>b</i> contents. While distilled water was applied to the control group, onion bulbs in the treatment groups were exposed to 1, 2.5, 5, 15, and 30 mg/L MCI/MI concentrations at 21°C in darkness for 3 days. Compared with the control, MCI/MI treatment caused dose-dependent reductions in root length, germination percentage, weight gain, and mitotic index values. Conversely, micronucleus frequency and chromosomal aberrations increased significantly with higher concentrations. Chromosomal abnormalities such as vagrant chromosomes, sticky chromosomes, pole flattening in anaphase, reverse polarization, unequal chromatin distribution, bridges, and vacuolated nuclei were observed. Anatomical analysis revealed epidermal cell deformation, nuclear flattening, cortex cell wall thickening, and indistinct vascular tissues. Biochemical findings indicated that enhanced superoxide dismutase and catalase activities were consistent with increased malondialdehyde and proline levels, while chlorophyll <i>a</i> and <i>b</i> contents declined with increasing doses. Although research on MCI/MI toxicity in plants is scarce and mostly focused on methylisothiazolinone alone, the present study highlights that MCI/MI exposure in <i>Allium cepa</i> provides critical insights for basic sciences and ecotoxicology.</p>