How morphological variability arises through evolution of developmental circuits is a central theme in developmental and evolutionary biology. On a shorter time scale such questions translate to (i) which developmental mechanisms are the basis of intraspecific variability and (ii) how this could be acted upon by natural selection and lead to adaptation in key functional traits and (iii) how this could be constrained in various ways. Here we present a project that takes advantage of the highly polymorphic fish species, Arctic charr (Salvelinus alpinus), and the recent advances in high throughput sequencing approach, to cast light on the developmental basis of variation in the trophic apparatus, focusing on the development of the jaws and pharyngeal arches and their adjoining muscles. To get the first glimpses into this developmental circuitry in a non-model species we sequenced transcriptomes of embryos from contrasting morphs at several developmental stages focusing our attention on mRNAs and micro-RNAs that showed differential expresion levels among morphs. We have identified thousands of transcripts that are differentially expressed among morps. We have also idendified 217 known miRNAs and 430 novel miRNA-candiates in the charr transcriptome, of which 25 and 7, respectively, were found to be differentially expressed among morphs. We are now focusing our attention on sub-sets of these genes that have been implicated as having a role in the formation of craniofacial elements and other key developmental processes in model species by (i) verifying the transcriptome results with qPCR, (ii) using in situ probes to elucidate the spatial expression patterns in embryos, (iii) using expression correlation analyses of developmental series and available databases to construct co-expression networks, and (iv) using de novo motif enrichment analyses for tightly co-expresses genes to identify potential transcription factors. The transcriptome also allows us to survey sequence variation in this important part of the genome. Among ca. 100.000 polymorphic sites we have identified 1300 candidate SNPs that are likely to show different frequencies among morphs.