A methodology to assess potential risks of releasing genetically modified organisms (GMO) to the environment was developed for the genus Cucurbita. Analysis of species biology (GMO, wild, and domesticated relatives) and their spatial distribution were considered. Biological information including reproductive systems, flowering and fructification patterns, pollination and dispersal mechanisms, genetic variability, hybridization and traits of the introduced gene, as well as environmental variables for the species were obtained. Spatial distributional patterns for these species were generated using distributed databases of herbaria specimens, environmental digital maps, and genetic algorithms. The risk of introducing a GMO of Cucurbita pepo in various localities of Mexico was analyzed for 15 taxa of this genus. A map of the potential spatial distribution of 'hot-spots' for the genus was obtained. Likewise, maps of the potential distribution of fertile progeny (F1) resulting from a theoretical random crossing over of the native species of Cucurbita were also obtained. Results showed there are regions where up to seven wild and domesticated species can converge, mainly in Tamaulipas, Veracruz, and the eastern and central parts of San Luis Potosí. The intended sites for release of virus resistant squash were located where several wild and domesticated species of cucurbits coexist. Results showed that the localities with greater risk are in Nuevo León, Sinaloa, and Guanajuato. These localities harbor wild relatives (free-living C. pepo, C. moschata, C. argyrosperma ssp. sororia, C. fraterna, and C. ficifolia) that are sexually compatible with the virus resistant squash. Therefore, any escape of the genetically modified squash would greatly affect the wild and domesticated species. Finally, the usefulness of this type of analysis for limiting releases of GMO within geographic areas of potential regions of crop domestication was discussed.