Population monitoring provides information on species conservation status. We reassess the status of the southern elephant seal population at Macquarie Island. The number of cows on the isthmus, ~20% of the total population, correlated with counts for the whole island (i.e. they reliably indicate island-wide trends). Cow numbers within the isthmus decreased from ~9400 in 1949 to ~2550 in 2023 at −1.1% year−1, similar to the −0.8% year−1 from 1984 to 2023 when counts were made annually (before 1984, counts were less systematic). This contrasts with all other southern elephant seal populations, which are either stable or increasing. There was also considerable year to year variability (± 350 cows year−1) in the numbers of cows ashore, indicating individuals skipping breeding. Counting errors may contribute to this variability but are unlikely given that the isthmus study area harems are small, typically < 200 cows. We found no link between cow numbers and summer ocean conditions using the Southern Annular Mode as a proxy (i.e. prior to blastocyst implantation), and it remains unclear what is causing this variation. Nonetheless, several other studies have suggested changing prey conditions during the winter are the most likely cause of this overall and ongoing decrease.