Background: American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible in this species. Instead, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms of eels from two geographic origins reared in controlled environments. Results: The null hypothesis of no difference of gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared in different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities. Conclusions: These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining the extent of differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of proportion of genes that are differentially expressed and the diversity of biological functions being involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels.