From 2003 to 2009, we surveyed Las Perlas Archipelago off the Pacific coast of Panama 53 times between the months of August and October to estimate abundance of humpback whales and to test for a migratory connection with populations from the southern hemisphere. We identified 295 individuals using photo-identification of dorsal fins, including 58 calves, and the population estimate for a single season was 100–300 solitary adults plus 25–50 mothers with calves; the estimated population of animals across all seasons using a mark and recapture model was over 1,000. Eight of the 139 fluke identifications were matched to whales in photograph catalogues from the Antarctic Peninsula and a ninth was matched to a whale sighted in Chilean waters; four of these nine individuals have also been sighted in Colombia. We conclude that Panama (Las Perlas Archipelago in particular) is an important calving area for humpback whales in the Southern Hemisphere. These data should provide a foundation for monitoring of population change and to increase awareness in Panama about the need to manage vessel traffic and tourism related to the whales at Las Perlas.