BACKGROUND: A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. RESULTS: Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, i.e. hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of co-expressed genes involved in phenotypic divergence and their key drivers, and further identified a module part specifically rewired in the backcross progeny. CONCLUSIONS: Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to BMP and Calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish.