Conserving life history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early, premature migrating and late, mature migrating forms of Chinook salmon face unequal pressure from natural and anthropogenic forces. These forces may result in the diminishment of migration variation in some stocks because migration timing is known to be highly heritable. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among the diverse populations of Chinook salmon. Therefore, application of this association for management may be premature. We examined the association of genetic variation in 28 markers on chromosome 28 surveyed with high-throughout genotyping (GT-seq) with individual run timing characteristics gleaned from passive integrated transponder recordings of over 5,000 Chinook salmon from the three phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them, the three lineages exhibited very similar genetic variants in the chromosome 28 region and moderate to strong association of these variants and run timing phenotypes. This is particularly notable for the interior stream-type lineage, which exhibits an earlier and more constrained migration of fish than the other lineages and which are exclusively premature when they enter freshwater. In both interior stream-type and interior-ocean type Chinook salmon, heterozygotes of the most strongly associated linkage groups are largely intermediate to homozygotes in migration timing, and while we make no robust conclusions about dominance, results indicate codominance or marginal partial dominance of the early migrating allele. Our results lend support to the cautious utilization of chromosome 28 variation in tracking and predicting run timing in these Chinook salmon.