Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of the Capitella telata and Helobdella robusta genomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leech H. robusta contains many more copies (12) of the sodium-potassium pump alpha subunit (Na+/K+-ATPase) gene than does the marine polychaete C. telata (2). The sodium-potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na+/K+-ATPase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na+/K+-ATPase duplications coincided with the marine-to-freshwater transition in Clitellata we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na+/K+-ATPase gene transcripts in order to infer the timing of gene duplication events using tree-based methods. The inferred timing of Na+/K+-ATPase duplication events is consistent with the timing of the initial marine-to-freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats.