Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a Quantitative Trait Locus (QTL) for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss. Among the genes located in the region of the major development rate QTL (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate QTL. In a follow up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate, and moreover found associations between development rate and allelic variation in all three candidate genes within the QTL for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life history diversity in this model salmonid.