Scientists in various subdisciplines of biology have long relied on model organisms to push the frontiers of knowledge forward as far as possible in their specific field. Today, interdisciplinary science requires model organisms that can push our understanding on multiple frontiers and help us formulate and address more complex questions. Members of the genus Daphnia represent just such an interdisciplinary model. Daphnia are aquatic microcrustaceans (also known as waterfleas) that have long been central to the study of ecology and toxicology and have recently been developed as a genomic model. A recent survey of both nuclear and mitochondrial markers in populations of the Daphnia pulex complex from high-altitude lakes in South America (Mergeay et al. 2008, this issue) provides an excellent example of how genetic data and ecological information can be used to push the boundaries of our understanding in molecular ecology. In this species complex, extensive hybridization has occurred resulting in polyploidization and, consequently, asexuality. Their data reveal high levels of genetic diversity, incongruence in phylogenetic signal among genomes (nuclear and mitochondrial), cryptic species in the complex, and a new model for the historical spread of the species throughout the Americas. Their data indicate that genome-level changes have occurred in this species which have profound consequences in an ecological context, the implications of which can be more fully appreciated because of our extensive knowledge of the ecology and natural history of the genus Daphnia.