Relatively little is known about the long-term response of Caribbean mangroves to human and natural disturbances during the ‘Little Ice Age’ (LIA). We present new palynological information on the dynamics of the Bahia Honda mangrove from the eastern coast of San Andres Island in the southwestern Caribbean for the late Holocene. Major changes in the Bahia Honda pollen record show the combined effects of natural events (strong storms and sea-level rise), and human disturbances. These changes are supported by ¹⁴C dates, sedimentological and palynological information. A storm (most probably a hurricane) was recorded around AD 1600, caused sediment reworking and the subsequent loss of about 2000 years of the vegetation record. The devastation of tree vegetation by this event allowed the expansion of heliophytic vegetation (e.g. grasses and vines). Mangroves and coastal vegetation started to recover at AD 1700, reaching their maximum extent within a few decades, when microforaminifera shells became abundant at the coring site, thus suggesting a relative sea-level rise because of the geomorphic reconfiguration of the coastal plain after the storm. Furthermore, the pollen evidence indicates more humid regional climates during the late LIA (AD 1700—1850). Mangrove and coastal vegetation declined sharply as a consequence of the establishment of coconut plantations around AD 1850. The recovery of the mangroves after AD 1960 is a result of the combined effect of relative sea-level rise and drastic changes in the local economy from coconut plantations to commerce.