Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific challenges including salt spray, temperature, water availability, and soil chemistry. Gene flow between locally adapted populations will effect genetic diversity in both local demes and across the larger meta-population. A single population of annual M. guttatus from Iron Mountain, Oregon (IM) has been extensively studied and we here building off this research by analyzing whole genome sequences from 34 inbred lines from IM in conjunction with sequences from 22 Mimulus individuals from across the geographic range. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high intra-population polymorphism (synonymous π = 0.033). Variation outside genes may be even higher, but is difficult to estimate because excessive divergence affects read mapping. Second, IM exhibits a significantly positive genome-wide average for Tajima’s D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in other species. Third, IM exhibits a distinctive haplotype structure. There is a genome-wide excess of positive associations between minor alleles; consistent with an important effect of gene flow from nearby Mimulus populations. The combination of multiple data types, including a novel, tree-based analytic method and estimates for structural polymorphism (inversions) from previous genetic mapping studies, illustrates how the balance of strong local selection, limited dispersal, and meta-population dynamics manifests across the genome.