Anti-Müllerian hormone (AMH) is a growth factor produced by granulosa cells that has an important role in regulation of ovarian follicle growth. Recent studies have shown a positive association between circulating AMH concentrations with number of follicles and oocytes in ovaries (ovarian reserve), response to superovulation and embryo production, fertility and herd longevity in dairy and beef cattle. The objectives of this study were to estimate the genomic heritability of AMH and identify candidate genes associated with AMH production. Serum concentrations of AMH were determined in 3092 dairy Holstein heifers (12–14 mo of age) from Green Meadows dairy farm in Elsie, Michigan. A total of 2939 Holstein heifers were genotyped for single nucleotide polymorphisms (SNP) using the Zoetis 70K SNP Panel. The genotypes were imputed to standard USDA 60,671 bovine SNP set; 54,519 SNP markers remained after standard editing procedures. A total of 2914 cows with both genotypes and phenotypes (AMH) were used for the analysis. A linear mixed model was used to model the random effects of sampling day and genomics on the logarithm of AMH. Results showed that the genomic heritability (±SEM) of AMH was 0.36 ± 0.03. We identified 12 significant SNP markers on chromosomes 11 and 20 based on a 5% false discovery rate which were mapped to 6 candidate genes using the ENSEMBL database implying these genes may have a role in AMH regulation. These candidate genes are linked to polycystic ovarian disease (DENND1A), steroidogenesis (NR5A1), embryo development (NR6A1), cell cycle regulation (PPP6C, RABGAP1), T cell development (LRRC8A). The high heritability and positive association of AMH with well-established reproductive traits implies that AMH can be used as a biomarker to improve reproductive potential in dairy cattle.