Analysis of biogeography patterns can provide insights into the underlying connectivity processes in an evolutionary context. The anemonefish complex, with 28 species distributed throughout most of the Indo-Pacific region, can be informative as a model group of studies of gene flow and evolutionary ecology. In this chapter, we assess the species boundaries and genetic relatedness of 13 species whose individual ranges span more than one of the six broad biogeographic regions defined for anemonefishes. We review the available studies that have examined gene flow within species. Some species seem to have evolved with clear species boundaries while others frequently demonstrate interspecific hybridization. Close examination of the ecology of anemonefishes could provide insight into the relative roles of micro- to macro-evolutionary processes. We discuss some ways in which carefully designed future works, using anemonefish as model species, could answer broader questions about evolutionary ecology. As in so many other aspects of marine biology and marine ecology, anemonefish have great potential as model systems for understanding biogeography and speciation.