Neotropical mangrove ecosystems have undergone drastic changes in terms of extension and floristic composition during Plio–Pleistocene times. It is unclear if the northern Pacific coast of Colombia has been occupied continuously by mangroves during the last 5000 years, or if their presence is a recent phenomenon. Two basic questions were asked: (1) is the establishment of mangroves recent?; and (2) what were the dominant floral taxa during the late Holocene? In the Gulf of Tribugá, northern Colombian Pacific, 22 sediment cores were drilled to a maximum depth of 2 m in a diverse suite of mangrove substrates and positions relative to the shoreline. Data were gathered from sedimentological descriptions, palynological analyses, and radiocarbon dating of these cores. During the last 4500 years, mangroves in the southern area of the Tribugá Gulf have remained floristically stable and dominated by Rhizophora. The abundant presence of Acrostichum aureum is recent, probably related to human activities. In contrast, two areas in the northern part of the Gulf show a different history. In the first area, the establishment of mangrove has been relatively recent (ca 2600 yr), probably a result of local subsidence due to tectonic faulting; this mangrove forest was and is dominated by Pelliciera rhizophorae. In the second area, mangrove pollen was not found in sediments younger than 2500 years, suggesting that the scarce presence of mangrove in the area is a result of recent colonization, and not due to logging as previously thought.