Gene flow is a major determinant of adaptation and has a large impact on biodiversity. E.g., local adaptation or spatial genetic diversification is impeded by gene flow between habitats. A simple way of measuring gene flow is to count the number of migrating organisms. However, there is a growing number of studies showing that gene flow can differ significantly from what would be expected measuring simply the number migrants. Hybrid incompatibilities and local adaptations usually reduce the gene flow between habitats, whereas heterosis (hybrid vigor) or sex ratio distortions cause an increase in gene flow. In the present study we introduce a new concept to describe gene flow, the “effective migration rate”. The “effective migration rate” was originally developed to describe gene flow through hybrid zones. Using simple mathematical models, we demonstrate that the concept of “effective migration rate” can be applied in various situations. Further, we present a simple and intuitive technique to obtain good approximations of the effective migration rate. We argue that the “effective migration rate” is a useful concept to measure gene flow, and of importance to both theory and empirical biology.