The green revolution has significantly helped in increasing the food production. So far, various breeding methods have been exploited, besides them recombination DNA technology provides another approach for increasing the food production. By means of this technology the losses in food production incurred by various biotic and abiotic stresses can be effectively controlled. In most of the transgenic studies scientists have used antibiotic resistant genes as markers for easy selection of transformants but there are risks involved in use of GM foods. To make such foods safer and environment friendly we have discussed a novel strategy i.e. Cre-lox which involves site specific recombination. By means of Cre-lox the marker genes can be specifically removed once the selection of transformants is over. In addition, this strategy can be used to module the hybrid chromosomes, avoid gene silencing and incorporate single copy of a transgene for its higher expression.