Our current standard of living depends on our ability to produce good quality affordable food, feed and fibre, while preserving the biosphere’s capacity to do the same for the next generations. Crop improvement will play a major role in solving this challenge, one of many we are currently facing. Modern biology has been contributing to crop improvement for decades, through better breeding methods and genetic engineering. The impact of agriculture on the environment has been massive; there are doubts about the sustainability of some current agricultural practices. While it is critical that any innovation we deploy improves sustainability, making decisions in this area is fraught with difficulties. Defining sustainability and identifying unsustainable practices is complex, context-dependent, and related to political, and socio-economic issues rather than to scientific and technical issues. The environmental safety issues raised are rarely specific of biotechnology. Biotechnological innovations in agriculture are mostly improved crops varieties, obtained through biology-assisted plant breeding or through genetic engineering. They will impact on the environment through the production system they are deployed in. This is the context in which the environmental safety of biotechnological innovations should be assessed and regulated. A narrow focus on biotechnology as a source of innovations “dangerous” for the environment runs the risk of missing other, possibly more important, environmental risk factors, and to delay or forego many environmental benefits biotechnology may offer. Harnessing better and wider genetic diversity to improve crops will contribute to a productive sustainable agriculture. Diversity Arrays Technology, a high-throughput high-resolution genome profiling methods can help plant breeders invent the safe improved varieties of tomorrow and monitor genetic diversity and gene flows.