Short-day photoperiod (SDPP; 8 h light:16 h dark) in the dry period increases milk yield in the subsequent lactation compared with long-day photoperiod (LDPP; 16 h light:8 h dark) in goats. Photoperiod, is the most potent environmental cue that entrains circadian clocks . Our previous studies showed that disruption of circadian clocks impact mammary proliferation, differentiation and milk yield. We therefore, hypothesized that photoperiod effects on lactation are mediated in part through the mammary circadian clock system. The current study aimed to investigate the effect of photoperiod on the mammary expression of the core clock genes: ARNTL, CLOCK, CRY1, CRY2, and PER1. To study these effects, 12 Israeli Saanen goats were blocked at dry off (~45 d prepartum) into 2 treatments of SDPP and LDPP. Two mammary biopsies were taken – one in the middle of the light phase and another in the middle of the dark phase – at approximately 3 wk prepartum and 5 wk postpartum. mRNA abundance of the core clock genes was measured using qPCR. Milk yield was greater (P < 0.0001) in SDPP than in LDPP (3.15 ± 0.04 vs. 2.7 ± 0.05 kg/d). PRL concentration was greater (P < 0.0001) in LDPP than in SDPP at 3 wk prepartum (823.4 ± 56 vs. 40.2 ± 10.2 ng/mL), 3 wk postpartum (471.3 ± 40.3 vs. 41.1 ± 5.75 ng/mL) and 5 wk postpartum (365.4 ± 26.6 vs. 20.9 ± 4.21 ng/mL). The light/dark schedule affected the relative expression of PER1, being greater in the light period (P = 0.003). Generally, there was a greater relative expression of CLOCK (P = 0.03), CRY1 (P = 0.04), CRY2 (P = 0.03), and PER1 (P = 0.02) in mammary of SDPP versus LDPP exposed goats. There was an increase in the expression of ARNTL (P = 0.014), CLOCK (P < 0.0001), CRY1 (P = 0.009), and CRY2 (P = 0.0001) from late pregnancy to lactation. Thus, homeorhetic changes associated with differences in photoperiod and physiological state are accompanied by changes in mammary circadian clocks. Since circadian clocks regulate cell proliferation and metabolism, there is the potential that changes in mammary core clock dynamics are regulating the photoperiod effects on milk yield in dairy goats.