The intraspecific movement of novel traits in agriculture involves a metapopulation that includes cropped, volunteer, and feral subpopulations as well as a latent population comprised of any viable seed anywhere within the agro-ecosystem and agricultural supply chain. An assessment of novel trait movement risk or containment requirements relies on a good understanding of volunteer and feral populations as well as a deep understanding of supply-chain operations, processes, protocols, and equipment. For coexistence scenarios where threshold levels are low, an assessment of the potential success of trait containment will be overestimated if there is a poor understanding of the species metapopulation. The biology and ecology of cropped species varies with respect to the potential for intraspecific trait movement, and some species, such as alfalfa, may pose a much greater challenge in terms of trait containment than spring wheat, for example, although agronomic practices do mitigate these differences and one should not assume that a species’ nature alone will determine trait containment. We show examples of this for canola, spring wheat, and alfalfa and explain the implications for coexistence in low level of presence scenarios.