Polyploidy, or whole-genome duplication (WGD), is a major evolutionary force with dramatic ecological and evolutionary repercussions. The impact of recurring WGD events on the genetics and ecology of naturally occurring allopolyploid species has been investigated for select taxa; however, multi-cytotype autopolyploid systems remain relatively understudied. Historically, it was believed that an autotetraploid had to outcompete its diploid progenitor to persist. Stebbins, for example, proposed that the formation and spread of an autotetraploid, although seldom successful, caused the diploid progenitor to become geographically restricted and rare. We now know that autopolyploids and their diploid progenitors can both remain extant and in some cases may coexist. We developed autopolyploid-aware theoretical models to investigate the ecological and evolutionary consequences of coexisting cytotypes with ongoing gene flow. Contrary to previous research, we found that long-run stable coexistence of cytotypes is possible under certain demographic and environmental conditions. Since coexistence among cytotypes is likely more extensive than currently recognized, we developed, and extensively tested, a new statistical approach for detecting mixed cytotypes in population genetic datasets. We also defined genetic expectations for multiple cytotype populations where coexistence is likely.