Specification of head structure as a result of changes in craniofacial architecture is a crucial step towards evolutionary adaptation. The head of teleost fish, particularly their trophic apparatus is one of the most complex integrated musculo-skeletal systems. The astounding craniofacial diversity in teleost fish provides an interesting model for studying these variations at evolutionary and developmental level. Arctic charr (Salvelinus alpinus) is amongst the most thoroughly studied systems exhibiting parallel evolution of benthic/limnetic morphological characteristics, particularly in the head and trophic apparatus. In Lake Thingvallavatn, four morphs of Arctic charr are found, two are benthic with subterminal mouth and blunt head (small and large benthivorous) and two are limnetic with elongate gracile terminal mouth (planktivorous and piscivorous). In this study the molecular basis of this craniofacial divergence during embryonic development was addressed by spatio-temporal expression profiling of candidate genes. We found a list of differentially expressed genes between benthic and limnetic morphs and a subset of the genes was shown to have craniofacial specific expression. Moreover, a network of genes with conserved co-expression in vertebrate was found to be differentially expressed in developing head of benthic and limentic morphs. Enrichment analysis of transcription factor binding site suggests a list of potential regulators for the network of co-expressed genes. These findings might be important to shed light on molecular mechanisms involved in vertebrate craniofacial evolution.