Sueste Bay, in the Fernando de Noronha archipelago (FNA), contains the only mangrove area among the oceanic islands of the South Atlantic. This work aims to reconstruct this mangrove's evolution during the Holocene based on a morphostratigraphic study integrated with palynological and multi-elemental geochemical data, temporally calibrated with radiocarbon dating. The data obtained indicated that, around 8000 to 7000 cal yr BP, well-developed Rhizophora and Laguncularia mangroves established over altered rocks of the Quixaba (phonolites, lamprophyres, basanites, trachyandesites and basalts) and Remédios (basanites, melilite and melanophelinites) Formation, under rising relative sea level, about 2 to 3 m below present. This period was the last record of Rhizophora in the FNA. From 6000 to 3600 cal yr BP, the lagoon system was eroded and significantly retrograded, under rising RSL during at least part of time, leaving clay pebbles scattered in the lower/upper shoreface deposit as the only record of its reworking. This process limited mud/mixed flats near the mouth of the Maceió River. Under a relative stability of RSL from 3600 cal yr BP to the present, a progradation of coastal facies, including beach/foredunes ridges, occurred and allowed the development of the modern lagoon system over swales between aeolian sand ridges. Mangroves were only observed during modern times but in environmental conditions very different from those of the previous occurrence. Indeed, Laguncularia coexists with several invasive plants within the narrow mixed flats associated with a small and almost filled tidal creek, whose siltation may be a product of the artificial damming of the Maceió River to supply public water to the archipelago. This study highlights the complex interactions between natural processes, sea-level changes, and human activities in shaping the coastal evolution of the Fernando de Noronha archipelago over the Holocene.