Recent advances in sequencing technologies, statistics and theory have advanced the field of population genetics. This special issue deals with the effective population size (Ne), an important parameter to predict evolutionary trajectories and to plan conservation actions. The effective size of populations can be estimated from genetic or from life history data and depends on a variety of parameters, such as the neighborhood of a population, or its mode of reproduction. Estimation methods have benefited from genome-wide genotyping and new estimation methods may be more precise and balanced. The contributions of this special issue provide improved ways to predict and estimate the effective population size in different situations and present applied studies where Ne was estimated in different natural settings. As such the special issue may serve as a resource and guideline, or as inspiration to population geneticists, researchers interested in microevolution and conservationists.