Harbour seals were extensively hunted in Denmark, but have only been driven to local extinction in one larger area, the South Funen Archipelago and Little Belt, where the species has been absent throughout the 20th century. Despite high growth rates of the Danish harbour seal populations after protection from hunting in 1976, seals have only been observed sporadically in the South Funen Archipelago and Little Belt until recent years, where recolonisation now causes conflicts with fisheries. Here, we review historical sources documenting the local extinction of harbour seals in the area during the 19th century and report the results of aerial surveys of haul-out sites during moulting seasons of 2021–2023 and pupping seasons of 2022 and 2023. Historical sources reveal that seal hunting was a common practice in southern Denmark, but catches dwindled to rarities during the 19th century. During recent surveys, seals were detected at six of the identified potential haul-out sites. Around Aarø Island, an average of 141 (range: 92–186) harbour seals were recorded over four moulting season surveys, constituting the majority (90%) of the total counts of the surveyed area. During the pupping seasons, a total of five pups was encountered at two different haulouts. As none of the haulouts are protected during the pupping and breeding seasons, protective measures may support this recolonisation of the historic harbour seal breeding range.