Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotypes on the same plant samples of Chrysolepis chrysophylla (Fagaceae; golden chinquapin) from 22 sites were used to determine genetic diversity and population structure. One site of C. sempervirens allowed interspecific vs. intraspecific comparison. SSRs and SNPs yielded many similar results. Among-site variation contributed 13% to 17% of the genetic variation and Fst estimates of 0.14 to 0.17 were in the range expected among Fagaceae species rather than among populations within a species. The northern sites tended to group separately on the first two axes of multivariate scatterplots from southern sites. Sites in two geographically isolated areas were divergent: 1) the Hood Canal, Washington population was relatively more genetically distant from other golden chinquapin sites than was our C. sempervirens site; 2) three coastal southern California sites were moderately diverged. The Hood Canal site had a negative inbreeding coefficient, fewer alleles, lower heterozygosity, and differed from the Skamania County, Washington site as well as all other sites. Hood Canal trees are distinguished by disjunct geography and by these molecular results. This suggests that the golden chinquapin near Hood Canal be treated as a management unit, and potential conservation actions are discussed.