|Abstract||The rainbow trout, Oncorhynchus mykiss, is a partially migratory organism used to study the genetic control of migration. Much of this research has taken place at a unique site in Sashin Creek, Alaska, where the resident and migrant O. mykiss populations are isolated from each other. However, it is unknown the extent to which findings here are shared with other populations. Here we used pooled sequencing to gather genomic data from 174 fish in two locations – Sashin Creek, Alaska and Little Sheep Creek, Oregon. Four sequenced pools were developed based on phenotype and population. We then measured differentiation between the populations to identify regions that may be associated with the resident or migratory phenotype. Our findings identified specific genes and chromosomal regions that may be important in the regulation of migratory tendency in this species, and indicate that there are population-specific controls that regulate migratory behavior.