Spatial heterogeneity in the environment induces variation in population demographic rates and dispersal patterns, which result in spatio-temporal variation in density and gene flow. Unfortunately, applying theory to learn about the role of spatial structure on populations has been hindered by the lack of mechanistic spatial models and inability to make precise observations of population structure. Spatial capture-recapture (SCR) represents an individual-based analytic framework for overcoming this fundamental obstacle that has limited the utility of ecological theory. SCR methods make explicit use of spatial encounter information on individuals in order to model density and other spatial aspects of animal population structure, and have been widely adopted in the last decade. We review the historical context and emerging developments in SCR models that enable the integration of explicit ecological hypotheses about landscape connectivity, movement, resource selection, and spatial variation in density, directly with individual encounter history data obtained by new technologies (e.g., camera trapping, non-invasive DNA sampling). We describe ways in which SCR methods stand to revolutionize the study of animal population ecology.