A hybrid lineage of Cottus fish has recently (less than 200 years) invaded vast habitats within the lower River Rhine basin, previously uninhabited by their parental species Cottus perifretum and Cottus rhenanus. Despite the lack of geographical and intrinsic barriers to reproduction, invasive hybrid fish appear to be isolated from both parental species. This suggests that adaptation to different habitats drives divergence, although, the nature of this is not known. Previous analyses of differential gene expression identified genes that are likely to contribute to adaptive changes in hybrid Cottus. However, it is not clear how tissue specific these patterns were and how variation in the environment affected the results. Here, we used microarray analyses and RNASeq to identify differentially expressed genes in fin and liver tissues collected from controlled laboratory environments and in different seasons (winter/summer). We found that overall gene expression patterns were specific to lineages, with parental species being the most different from each other and hybrids showing intermediate phenotypes. Moreover, certain patterns of gene expression are consistently differentiating the hybrid lineage from both parental species. It is likely that the latter constitute fixed traits of the hybrid lineage. These traits may be most relevant to understand the rapid divergence between parents and hybrids and can give insight on the onset of hybrid speciation in nature.