In Canada, the monarch butterfly, Danaus plexippus (L.), is designated a species of “special concern.” During their southward journey each year, hundreds of thousands of monarchs funnel through Long Point, Lake Erie in Canada. Standardized daily counts of migrating monarchs have been conducted at two sites on Long Point for 20 consecutive years (1995–2014). Using a Bayesian framework, we estimated long-term trends in the number of migrants passing through Long Point. Over the 20-yr period, credible intervals for trends estimated at each site overlapped, with an estimated decline of 5.11%yr-1 across sites. However, trajectories differed between sites. At the more inland site, a more constant 7.78%yr-1 decline was detected, but at the tip of the peninsula, counts increased by 10.04%yr-1 from 1995–2005, followed by a decline of 11.9%yr-1 from 2004–2014. This resulted in an estimated 20-yr decline of 2.74%yr-1 at this site. Lower and less variable counts since 2010 appear to be driving the apparent long-term population declines. Relative to the tip site, counts from the more inland site are less likely to be biased by large accumulations of monarchs blown off-course during headwinds or stopping over to replenish fuel supplies. Trends from the more inland site also show strong correspondence with declines in egg production and milkweed abundance in the upper Midwest, which suggests that the number of individuals counted on migration is evidence of a potentially broader-scale condition. Additional years of data should be collected to determine whether the apparent decline will continue.