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I examined the genetic architecture and evolutionary significance of the considerable morphological and life history variation in Arctic charr (Salvelinus alpinus) from natural and cultured populations in Iceland. I found that the sex determining locus in Icelandic Arctic charr is located on a different linkage group relative to the majority of the Atlantic lineage Arctic charr, including populations from the Fraser River in Labrador Canada and Swedish and Norwegian strains. In addition, there may be a possible conservation of a sex linkage arrangement in Icelandic Arctic charr and Atlantic salmon. These observations suggest that the differentiation of the sex determination chromosome in salmonids is still in the early stages. I then tested hypotheses regarding the genetic architecture of wild and cultured populations of Icelandic Arctic charr identifying the number and effect size of quantitative trait loci (QTL) and their conservation within and across salmonid species. QTL with genome-wide significance for body size, condition factor and age of maturation in cultured fish from the Icelandic breeding program were detected on multiple linkage groups. Comparisons with a North American cultured strain of Arctic charr and North American populations of Atlantic salmon and rainbow trout revealed some conservation in QTL. Additionally, I compared the genetic architecture of fork lengths in juvenile wild and cultured populations and found moderate conservation of genomic regions among Icelandic populations. I compared linear measurements taken on the cleared and stained heads of benthic and limnetic morphs from two lake populations expressing varying degrees of divergence. I found high genetic variation for craniofacial morphology in all morphs with no significant difference of plasticity levels between them. However, stronger family effects and weaker morph effects in the less derived lake population suggest higher genetic variation for craniofacial traits compared to the more derived system. Overall QTL (suggestive and significant) number and effect size was similar but the morphs hypothesized to be more derived within each lake had about half the number of significant QTL (p