Main challenges facing the researchers today is the rigorous assessment of the gene flow from the genetically modified organisms to microbial community, others commercial crops, wild relatives and weeds. Although transgenic crops benefit the society, the introduction of the transgenic crop into the food system has raised number of questions regarding the possible negative effects. The concern not only relegated to the field of plant scientists and activists, but also with the realm of the biomedical sciences in the aspects of allergenicity, assessing nutritional benefit, evaluating nutritional quality, meeting the nutritional needs of developing nations, and expanding the sustainable food supply to meet future demands. Food hazard of the transgenic is concerned mainly with the mechanisms such as the expression of the inserted genes, its secondary effects of gene expression, and insertional mutagenesis of the gene. The main focus is thus done on these areas to view the in-depth knowledge of the gene flow consequences. According to National Research Commission, the environmental hazard of gene flow leads to resistance evolution against herbicide, virus and insect/pest, movement of genes and non-target effects. Horizontal gene transfer of bacteria takes place by means of transformation, transduction and conjugation, which occurs mainly in prokaryotes, and is considered to be an important and dominant force in shaping the evolution of the genome. Public concern regarding the transgenic crop is still under controversial debate, so education and familiarization of the genetically modified products with the public will enable them to accept the gene technology concept and will put an end to this controversy in minor sense.