Micro-RNAs (miRNAs) have emerged as a major class of developmental regulators. Although the sequences of many miRNAs are highly conserved in evolution, they often exhibit temporal and spatial differences in expression during development.  The extensive trophic polymorphism seen in Icelandic Arctic charr offers a unique possibility for studying the role of developmental mechanisms in adaptive divergence. In this study we focus on differential miRNA expression during embryonic development of two contrasting morphs of Arctic charr, a small benthic morph from Lake Thingvallavatn (SB) and fish from aquaculture stock (AC). These morphs differ largely in morphology, body size and coloration. We sampled each offspring group at 4 developmental time-points for high-throughput small-RNA sequencing. We identified a total of 217 conserved and 430 novel miRNA candidates, of which 25 of the known and 7 of the novel miRNA candidates were found to be differently expressed between the two contrasting Arctic charr morphs. Three of the novel miRNA candidates were only detected in AC whereas one putative miRNA was only expressed in SB. MiRNAs such as miR-130, 153, 17, 30b, 451, 219, 133, 26c, 199a and 145 were highly expressed in AC, whereas miR-146, 183, 206, 135b, 122, 196a and 135b were highly expressed in SB. The majority of these miRNAs have previously been shown to be involved in various developmental processes in other species, e.g. development of brain and sensory epithelia, skeletogenesis and myogenesis. We also found that 84 known and 37 novel miRNA candidates were differentially expressed among developmental stages. Based on expression levels and known roles 9 miRNAs were selected for more detailed expression studies throughout development using qPCR and 3 were further studied with in situ hybridization. Finally we studied the allelic variation of the genomic regions surrounding some interesting miRNA candidates in 3 of the Þingvallavatn morphs.