The potential for genetically modified (GM) crops to threaten biodiversity conservation and sustainable agriculture is substantial. Megadiverse countries and centers of origin and/or diversity of crop species are particularly vulnerable regions. The future of sustainable agriculture may be irreversibly jeopardized by contamination of in situ preserved genetic resources threatening a strategic resource for the world's food security. Because GM crops are truly biological novelties, their release into the environment poses concerns about the unpredictable ecological and evolutionary responses that GM species themselves and the interacting biota may express in the medium and long term. One of the consequences of these processes may be a generalized contamination of natural flora by GM traits and a degradation and erosion of the commonly owned genetic resources available today for agricultural development. GM plants carrying pharmaceutical and industrial traits will pose even more dangerous risks if released in the environment.