Maternal diet has been shown to impact fetal development across a variety of species. Given the reported effects of omega-3 long-chain polyunsaturated fatty acid (n-3 LCPUFA) supplementation on health across species, it was hypothesized that supplementation of algal-based n-3 LCPUFA to mares around conception would alter the maternal uterine environment and modify gene expression in early conceptuses. Nonlactating, light horse mares were supplemented with concentrate (n = 6) or an isocaloric diet containing 0.06 g/kg body weight n-3 LCPUFA (primarily docosahexaenoic acid [DHA], n = 7) at least 60 days before first sample collection. Four consecutive ovulatory cycles were monitored. Uterine endometrial samples were obtained 12.5 days postovulation from cycles 1 (uninseminated), 3, and 4 (bred to a common stallion); embryos were flushed from cycles 3 and 4. Biopsies from supplemented mares were greater in DHA and total omega-3 fatty acid concentrations (P < .05), indicating successful tissue incorporation. Uninseminated n-3 LCPUFA supplemented mares displayed increased PTGFS and reduced IL6 gene expression (P < .01) than controls. Supplemented pregnant mares had increased mRNA abundance of PTGES (P = .05), PTGFS (P = .03), and SLCO2A1 (P = .01), while supplemented barren mares exhibited lower PTGFS (P = .05) and IL6 (P < .01) expression than control mares. In the conceptus, relative transcript abundance of trophoblast and endoderm markers (GATA3, GATA4, GATA6, TFAP2A, ELF3) was greater (P < .05) in embryos from supplemented mares. These results indicate algae-derived n-3 LCPUFA supplementation prior to breeding alters the maternal uterine environment and modifies expression of genes in preimplantation equine conceptuses.