Island populations have a much higher risk of extinction than their mainland counterparts for a number of reasons. Particular concern has been voiced that gene flow and hybridization between agricultural crops and native plant species may exacerbate their precarious position, especially if the gene flow occurs from crops developed through recombinant DNA technologies. Horizontal gene transfer (HGT) and vertical gene transfer (VGT) are the two possible ways for gene flow and introgression to occur. VGT is more likely to facilitate gene transfer between agricultural crops and native plant species, although this too is dependent on a variety of factors. In this critical review phylogenetic tribal boundaries were used as a limit to hybridization potential. Overlap was found between agricultural crops and native species in four tribes: Heliantheae, Gossypieae, Solaneae, and Phaseoleae. In each tribe the factors which increase and decrease the likelihood of hybridization were evaluated and distribution analyses performed. In general, it is concluded that hybridization potentials are low for most species (except Gossypium tomentosum that is known to hybridize with its cultivated relatives), however, small scale pollination studies should be performed for each tribe to quantify the risk and to better manage populations of native species.