Residual chlorine resulting from treatment of drinking water may be an unrecognized source of abiotic stress in agrosystems. This study aimed to, using a integrated morphological and RAPD-PCR method, analyse the dose-dependent effects of sodium hypochlorite on morphological performance and genomic stability of broad bean (Vicia faba L.). Seeds were treated with five different chlorine levels (0.5, 1, 2.5, 5 and 10 mg l −1) and a control treatment irrigated with river water. Morphological characteristics, such as height of plants, leaf number, branching, flowering and leaf size were recorded while molecular changes were screened by ten RAPD primers. The outcomes indicated that all vegetative growth parameters decreased significantly (p ≤ 0.05) with increasing concentration of chlorine and severe inhibition was detected at 5 mg/l and sometimes =>10 mg/l whereas low exposure to chlorine (1 mg/l) caused slight stimulation in branching of tomato with no stimulating effect on foliage count as evidence for manifestation of hormesis response. RAPD analysis indicated that significant genomic instability occurred under high dose of chlorine, including new appearance and absent bands of DNA and its variation being 77%-100%. The number of unique RAPD bands also increased with increasing chlorine concentration; indicating that the genotoxic effects were dose-dependent. These results indicate that NaOCl has a dual action in broad bean, i.e., an enhancing effect at low doses and morphological inhibition and genomic instability under high dose. RAPD markers were found to be sensitive in the early detection of genotoxic stress caused by chlorine and it emphasized the necessity of controlling residual chlorine in irrigation water for crop genetic integrity.