Radioactive pollution comes on the top of pollution types that affect human life directly through damaging the human genome or indirectly via his food web. The current study focused on the evaluation of radiation effects of Assiut Thermal Power Plant (ATPP) ashes on two crop plants, potato and squash, in terms of morphological and molecular levels. More particularly, the specific activity concentrations were measured in Bq/kg, of the 238U (226Ra) and 232Th series, and 40K-isotope for the untreated soil sample (control) and ATPP ash sample (represents the radioactive source with 100% concentration). Different concentrations of ATPP ash (0, 2, 4, 6 and 8%) were mixed with soil sample to study the effect of radioactively contaminated soil on potato and squash plants. The results of the present investigation revealed that the morphological characteristics of both potato and squash plants were changed, which reflected a steep regression in the values of all vegetative growth and yield traits. The alterations of the characteristic values were directly proportional to the radioactive ash concentration in the soil. In the same context, the molecular evaluation using PCR-based markers, e.g., ISSR and SCoT helps in understanding and explaining experimental observations at morphological level. ISSR/SCoT bands confirmed the toxicity and mutagenicity of radioactive ash samples at their present dose on both potato and squash plants. The present findings clearly explained the morphometric and genetic abnormalities in two of the main consumed crops by a human. Thus, the green area around the ATPP may disappear in the future due to increasing the pollution in terms of the radioactive component that directly attached to plants or indirectly by mixing with soil.