AbstractThis is the first morpho‐histological comparison of guanaco ovaries between reproductive (long‐days) and non‐reproductive (short‐days) seasons, and oestrogen receptor‐alpha (ERα) and beta (ERβ) detection. Different stages of follicle development were found in the cortical area, but no corpus luteum was detected. The size and frequency of antral follicles and large atretic follicles were higher in long‐day ovaries than short‐days, consistent with ovarian activity in this season. Differential expression of ERα and ERβ was observed in follicles at different stages of development between short and long days. These data reveal histological and molecular differences between reproductive and non‐reproductive seasons of guanaco ovaries.