The European eel Anguilla anguilla is an intriguing model in which to study olfaction because of its complex life cycle that includes two long distance migrations across the Atlantic, because it occupies an early branching position within the teleost phylogeny and because it is possible to maintain separate life stages in the lab. A. anguilla is also an important aquaculture species. In addition, several lines of evidence suggest that functional demands on the eel olfactory system are different and different life stages. Therefore, the goal of this research was to identify receptors and signal transduction genes that appear to have stage specific functions. If a gene has a stage specific role, it is expected to be expressed at higher levels at this stage. To test this hypothesis, we used a deep sequencing approach to first assemble the transcriptome of the olfactory epithelium the identify differentially expressed transcripts in immature males kept in freshwater or seawater and in sexually mature males. We found that the biggest shift in gene expression occurred in sexually mature males when a significant number of protein coding transcripts were down-regulated. In contrast, we found that a set of receptors involved in odorant/pheromone detection and G protein-coupled receptor (GPCR) signal transduction were up-regulated at this stage. We also found that overall, receptor expression was higher at the seawater stages (immature and sexually mature) than at the freshwater stage. Our data show that individual receptors from large chemosensory gene families exhibit life-stage specific expression patterns in eels indicating that specific receptors within these large gene families help animals adapt to specific life stage requirements including changes in environment.