Geographic patterns of species richness have been linked to many physical and biological drivers. In this study, we document and explain gradients of species richness for native and introduced freshwater fish in Chilean lakes. We focus on the role of the physical environment to explain native richness patterns. For patterns of introduced salmonid richness and dominance, we also examine the biotic resistance and human activity hypotheses. We were particularly interested in identifying the factors that best explain the persistence of salmonid-free lakes in Patagonia.