In the U.S., the Pacific Northwest (PNW) is the only area suitable for spinach (Spinacia oleracea L.) seed production. Fusarium wilt, caused by Fusarium oxysporum f. sp. spinaciae (Fos), is responsible for major losses in PNW spinach seed production. Most parental lines used in hybrid spinach seed crops are very susceptible to Fos. Genome wide association studies (GWAS) were initiated to identify sources of resistance to Fos. Spinach genotypes (n = 351) were evaluated for reactions to Fos using moderate and high inoculum levels from a mix of three isolates (Fus058, Fus254, and Fus322), with two replicates of a factorial design of genotypes and inoculum levels. A Fusarium wilt severity index (FWSI, 0 to 1) and area under the disease progress curve (AUDPC) calculated for wilt severity rated 21, 28, and 35 days after planting (DAP) in moderate risk soil ranged from 0 to 0.95 and 0 to 10.8, respectively. SNP markers (7,887) identified with genotyping by sequencing were used for marker-trait association with mixed linear model (MLM) in TASSEL 5.2.51. Population structure analysis showed two subpopulations (Q1 = 35.8%, Q2= 34.4%), with 29.6% of accessions showing admixture. Nine SNPs were associated with AUDPC in moderate risk soil (R² = 3.8 to 9.3%, -log P = 3.01 to 5.06). Five SNPs also were associated with FWSI 35 DAP (R² = 4.4 to 6.7%, -log P = 3.22 to 5.35). The SNPs may be used to develop high-throughput markers to breed for Fusarium wilt resistance in spinach.