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Palynological analysis of seventy-seven cutting samples from six boreholes in the Marañón Basin (northeastern Peru) has identified five distinct Neogene marine incursion events (ME-1 to ME-5), challenging existing models that depict them as short-lived episodes. The diverse palynological assemblages, comprising spores, pollen, freshwater algae, and critical marine indicators—including dinoflagellate cysts, foraminiferal test linings, and copepod eggs—reveal that these incursions were protracted and recurrent, each associated with a maximum flooding surface and bounded by intervals of continental sedimentation. The stratigraphic record shows the earliest event ME-1 (Aquitanian to Late Burdigalian, 23.03–17.7 Ma) identified across all studied wells. ME-2 (latest Burdigalian to Middle Langhian, 17.0–16.1 Ma) is also recorded basin-wide. ME-3 (latest Burdigalian to earliest Langhian 16.5–15.7 Ma) registered in two wells. ME-4 (Late Langhian to latest Serravallian, 14.6–11.62 Ma) registered in only two wells and ME-5 (Early Tortonian, 11.6–10 Ma) is documented exclusively in the southernmost well, culminating in Zanclean (~5.5–3.6 Ma) mangrove development. We interpret the ingress routes for ME-1 to ME-3 to be westward via the Marañón Portal or northward from the Caribbean, associating them with the Proto-Pebas and Pebas systems. In contrast, ME-4 would also be from Amazon trunk or Paraná Portal associated with the Pebas Phase, and ME-5 likely originated from the south through the Paraná Portal, linking it to the Acre Phase. These results demonstrate that Miocene marine incursions into western Amazonia were not brief episodes but represented prolonged periods of marine influence, facilitated by sustained subsidence in the Marañón retro-arc foreland basin. This history reveals a dynamic connectivity throughout the Neogene, with marine conditions acting as persistent biogeographic barriers that critically shaped the region’s Miocene biodiversity patterns. This refined chronology provides a comprehensive regional framework, significantly advancing our understanding of Amazonian paleogeography.