Here we investigate life history variation in Oncorhynchus mykiss in California's Eel River by using Rapture sequencing, on thousands of juveniles, to genotype the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy (OMY5) as well as determine patterns of overall genetic differentiation. The results presented in this study provide valuable information for designing future restoration and management strategies for O. mykiss in Northern California and beyond.