A key to understanding the origin and maintenance of the diversity of life is to understand how phenotypic and genetic variation is partitioned within and among populations. I characterize the spatial partitioning of phenotypic and genetic variation in an old Willamette Basin freshwater distribution of threespine stickleback (Gasterosteus aculeatus) and compare these results to younger populations. Phenotypic variation was measured using 14 phenotypic traits, and genetic variation was assessed using RADseq and Stacks software to identify tens of thousands of single nucleotide polymorphisms. The major partitioning of phenotypic and genetic variation in Oregon is along a stereotypical transition from oceanic to freshwater that has been seen in younger systems. Phenotypic and genetic variation is significantly partitioned between basin populations, and the genetic variation is geographically structured. This work suggests that parallel divergence between oceanic and freshwater forms originated before the end of the last glacial maximum.