This special feature: Genetic Structure and Adaptation in Coastal Ecosystems emphasizes the importance of research focused on population genetic structure and evolutionary change for understanding estuarine and coastal communities. Many studies have examined the effect of environmental gradients on community-level patterns in estuarine habitats; however, relatively little is known about the role of genetically based adaptation (the heritable response to these environmental gradients) in these organisms. This special feature presents 11 studies that use a variety of approaches including ecophysiology, ecological genetics, molecular markers, and patterns of gene expression occurring within these populations. These studies provide examples of the role of genetic diversity and adaptation across a diversity of estuarine and coastal environments, and highlight the temporal and spatial scales at which adaptation impinges upon management. This collection of papers is especially timely, given the increasing importance of understanding and predicting the response to global climate change in order to effectively manage these communities.