Environmental contamination by cadmium (Cd) and copper (Cu) threatens ecosystems and agricultural productivity due to their genotoxic impacts on plants. This study investigates the mitodepressive and clastogenic effects of Cd and Cu on Matricaria chamomilla L., a pharmacologically significant species with unexplored cytogenetic responses to heavy metals. Root meristematic cells were exposed to 50–200 ppm CdCl₂ and CuCl₂ to assess mitotic index (MI), chromosomal aberrations, and comparative metal toxicity. Mitotic abnormalities, including sticky chromosomes, laggards, bridges, micronuclei, and precocious movements, were analyzed alongside MI and Total Abnormality Percentage (TAP). Results revealed a dose-dependent decline in MI (Cd: 14.0 ± 0.36 to 7.15 ± 0.12; Cu: 15.13 ± 0.12 to 9.21 ± 0.18) and a rise in TAP (Cd: 3.37 ± 0.2 to 7.33 ± 0.14; Cu: 1.9 ± 0.23 to 5.51 ± 0.17). Cd exhibited greater toxicity, inducing higher abnormality frequencies than Cu. Chromosomal stickiness dominated anomalies, followed by laggards, bridges, and micronuclei, with Cd causing more severe disruptions to spindle dynamics and chromosome segregation. Control cells (MI: 16.51 ± 0.12) showed negligible aberrations. These findings underscore M. chamomilla’s sensitivity to metal-induced genotoxicity, validating its role as a bioindicator for pollution monitoring. The pronounced cytogenetic damage at elevated metal concentrations highlights ecological risks posed by Cd and Cu contamination. This study advances understanding of interspecific metal toxicity mechanisms and supports the integration of cytogenetic assays in environmental risk assessments, offering insights for phytoremediation strategies and heavy metal pollution management in agro-ecosystems.