High rates of self-fertilization have long been associated with weediness in plants. Complete self-fertilization prevents effective genetic recombination, reducing effective population sizes by one half, theoretically reducing genetic variation present in populations. However, predominantly self-fertilizing plants such as downy brome (Bromus tectorum) have been successful in adapting to and subsequently invading many environments or adapting to management inputs. They often have adaptively relevant levels of multi-locus standing genetic variation manifests as phenotypic variation within a single locale of the invaded range. How populations of predominantly self-fertilizing species maintain genetic variation within locales remains unclear. A single locus, self-fertilizing, two-island Fisher-Wright forward genetic simulation with migration was used to explore fundamental questions about the implications of self-fertilization, selection, and migration on the maintenance of genetic/phenotypic variation in populations of annual self-fertilizing weeds species. The Fisher-Wright simulation demonstrated that with migration between locales and differential selection on the allelic state within locales, genetic variation could be maintained indefinitely within locales. Our study corroborates the use of best management practices for minimizing or preventing seed spread that are recommended for the management of herbicide resistance, such as cleaning vehicles or equipment that is transported between sites.