The feature of living organisms stem from their genetic potential which is called genome. By changing the sequence and number of the four nucleotides that form the genome, various organisms are created. In different cellular conditions, the three-dimensional structure of the genome is changed and the expression of the genes are also altered; therefore genome can be considered as an ecosystem. The processing of the genomic ecosystem, like any other ecosystems, is necessary in order to better understand the more appropriate productivity. On the other hand, breeding of plants and livestocks as a genome manipulation is essential due to rapid growth of the population. By modifying a specific trait or gene at the time of manipulation, other traits and genes may be changed, after which a long and costly process is required to reduce the impurities. In this process, ecosystem of the genome and the expression of different genes can be permuted, which cause different complications. Effort to increase the yields while disregarding the native and modified resistant plants, leads to the degradation of the ecosystem. Also, one of the main concerns in some communities is health problems, such as the deficiency of certain vitamins, which can be resolved through the use of modern biotechnology. With the progression of biotechnology, not only the limitations of genome modification will be eliminated, but it is also possible to edit specific genome section that minimized the adverse impact on genome ecosystem and maximized its benefits.