Epigenetics includes the study of external factors that can influence the expression of genes by altering the accessibility of DNA through methylation. To investigate the epigenetic influence of season, sperm head shape, and semen storage on placental and fetal tissues, pregnancies were generated in the summer or winter using boar semen from either least or most sperm head shape change, collected during cool or warm seasons, and stored as cooled‐extended or cryopreserved. The lowest (p < 0.05) ratios of 5‐methylcytosine to 5‐hydroxymethylcytosine activity (5mC:5hmC) in fetal liver were from summer breedings and in placental tissues from winter breedings. The relative expression of placental
CDH1 tended (
p < 0.10) to be greater in placenta generated from cryopreserved semen or semen collected during cool periods. The relative expression of placental
GNAS was affected (
p < 0.05) by the interaction of breeding and semen collection seasons. Cryopreserved semen increased (
p < 0.05) the placental relative expression of
GNAS. Placental
MEST and
RHOBTB3 tended (
p < 0.10) to have a greater relative expression from pregnancies generated using semen collected during cool periods used during winter breedings. Within fetal liver, the relative expression of
GNAS and
HGF was greater (
p < 0.05) from winter breedings. Interaction of winter breedings and least sperm head shape change tended (
p < 0.10) to have the greatest fetal liver expression of
CDH1. Seasonality of semen collection, breeding, and the effect on sperm head shape change had an influence on the expression of genes with known differentially methylated regions or response to methylation activity from embryonic and extraembryonic tissues.