In the last half century, gene flow has moved from relative obscurity to a well‐recognized component of evolution. Gene flow, the successful transfer of alleles from one population to another, is now known to vary considerably among species, populations, and individuals as well as over time. It frequently occurs at rates sufficient to play an important evolutionary role for populations of both animals and plants (Ellstrand 2014; Yakimowski and Rieseberg 2014; Arnold 2015). Gene flow does not automatically come to mind in the context of evolutionary applications. When the senior author shared the idea of a Special Issue on Gene Flow in Applied Evolution with a colleague, she asked, “What else is there besides crop breeding?” Considerably more, as we shall soon see. Gene flow is important in a remarkable variety of applied situations. This Special Issue presents some representative points in the galaxy of applied topics in which gene flow plays a key role. The number of possible topics precludes an exhaustive treatment. Likewise, while we acknowledge that non‐sexual gene flow (horizontal transfer) has considerable applied and evolutionary significance in prokaryotes and eukaryotes (e.g. Koonin et al. 2001; Richardson and Palmer 2007; Arnold 2015), the topic is so large, we deem it worthy of separate treatment.