Inter simple sequence repeats (ISSR) or microsatellite markers were applied to assess genetic diversity induced in Allium cepa L. by drainage water and genetic relationship among five water resources which reflected water quality. Genomic DNA was extracted from fresh onion roots treated with drainage water from five resources. Six ISSR primers were initially used for screening water quality. Polymorphisms became evident through the presence and / or absence of DNA fragments in treated roots compared with the control treated with Nile River water. There was a distinct distance between the band profiles of treated roots and the control samples. When the cluster analysis was applied. The total number of bands generated by ISSR-3 molecular marker quality. This marker can be considered as a best reproducible primer to be used for screening water quality. This marker disappeared some bands depending on drainage water carrying toxicants. Similarity coefficients between different water resources was ranged from  0.76 to 0.98. The highest similarity coefficient was obtained between the drainage water from chemical fertilizer industry and oils and soap effluents. The lowest similarity was shown Nile River water and oils and soap industrial effluents. Number of polymorphic bands detected through six primers ranged from 3 to 10, whereas the unique fragments were ranged from 0 to 3. Finally , comparison between Nile River water treatment and treated genomes with drainage water shows that ISSR analysis can be used to evaluate the modifications induced in DNA structure in living organisms by drainage water carrying environmental pollution.