The Wallacea hosts a unique and largely endemic animal fauna, with high degrees of endemism. Sulawesi’s ichthyofauna represents an ideal study system to shed light on the ecological factors that determine diversity and composition of freshwater fishes, and the underlying evolutionary mechanisms. We analyze stream fish assemblages across different regions on Sulawesi by employing a combination of morphology-based analyses of ecologically relevant traits and genetic analyses, and combine these with estimators for resource use.