Parasitism is ubiquitous, yet little is known about the evolutionary mechanisms that lead to a parasitic lifestyle. Facultative parasites can switch between free-living and parasitic lifestyles, which may provide an opportunity for researchers to study the genetic mechanisms underlying a transition to parasitism. The oligochaete Dero (Allodero) hylae is a facultative parasite commonly found within the ureter of various anuran species, such as the Cuban tree frog (Osteopilus septentrionalis). The Dero hylae worm passes into the frog's cloaca, where it then infects the ureter. In the ureter, the worm loses its free-living characteristics such as hair setae, dorsal setae, a digestive tract, and fossa with gills as it transitions to a parasitic lifestyle. The parasite may be expelled from its host during urination, and when this occurs the worm will reacquire its free-living characteristics. The focus of this study was to compare the differential gene expression profiles observed when this rapid morphological change takes place. Specimens of D. hylae were extracted from wild Cuban tree frogs and either flash-frozen to capture the parasitic RNA gene expression profile or cultured for 2 wk and allowed to metamorphose to their free-living stage and then flash-frozen. The extracted RNA was used for de novo transcriptome assembly, and we conducted a differential gene expression analysis using an RNA Tag-Seq approach for both the free-living and parasitic life forms. Based on these results, we identified 213 differentially expressed transcripts between the 2 developmental forms, with 190 of these up-regulated in the free-living life form. Although over half of the differential genes recovered did not result in any significant BLAST hits, many of these genes did provide insight into which molecular signals are potentially used after the parasite transforms into the free-living form. This analysis provides significant insight into differentially expressed transcripts associated with the drastic morphological changes observed in this rare case of oligochaete parasitism by D. hylae encompassing both free-living and parasitic forms.