Climatic changes and sea level variations have had a significant impact on the mangroves along the Brazilian coast during the Holocene. The present study focused on understanding the specific factors that have determined the establishment and expansion of mangroves in a subtropical estuary of southern Brazil (Babitonga Bay, State of Santa Catarina-SC), as well as their response to climate change and sea level variations during the late-Holocene. In this study, we carried out sedimentary analysis, palynology, and radiocarbon dating (C-14) to paleoenvironmental reconstruction of the last 1500 cal. year BP. Three facies associations were identified, indicating a progradational succession where a tidal flat was developed at the margin of the estuary. During the first phase, between at least 1440 and ±1286 cal. year BP, the area was characterized by a subtidal environment. The presence of Laguncularia pollen grains since ± 1390 cal. year BP indicated favorable conditions for mangrove establishment in proximity to the study site. Subsequently, around ± 1286 cal. year BP, the tidal flat developed, reaching the present-day shoreline, facilitated by the relative sea level drop. Avicennia trees were established on the tidal flat since ± 1273 cal. year BP, and the establishment of Rhizophora trees occurred in the most recent decades. This mangrove succession developed in Babitonga Bay following a temperature gradient, associated with low-temperature tolerance, and likely its establishment is associated with a temperature increase during the late-Holocene, that caused a migration of the southern limit of the mangrove in the subtropical zone to higher latitudes. Furthermore, the relatively slow expansion of mangroves upstream of Babitonga Bay also may have been controlled by the suitable salinity and substrate conditions, which were favored by the relative sea-level fall during the late-Holocene.