The present study investigates the cytotoxic and genotoxic effects of two frequently employed synthetic food colorants, lemon yellow and orange red, using an Allium cepa assay. Uptake of food colorants by root cells at different concentrations and varied exposures significantly altered the cytogenetic system, membrane integrity, mitochondrial function, root growth, and cell division. The food colorants induced significant DNA damage, micronucleus formation, and other severe chromosomal aberrations at genetic level and inhibited cell division as well as root growth. Severe DNA damage, membrane damage, and metabolic inactivation observed in the result are indicative of apoptotic cell death. These results confirm the possible dose-dependent toxicity of these food colorants in plant systems. The chromosomes of plants and animals are morphologically similar and appear to respond towards mutagens in a similar way like mammals, indicating possible damage to the DNA of humans when these colorants are used indiscriminately.