Analyses of marine palynomorphs, including dinocysts and acritarchs, from Pliocene-Pleistocene sediments of the Ocean Drilling Program (ODP) Site 887 in the Gulf of Alaska allowed the development of a biostratigraphic scheme, which we compared with bio-events in regional diatom and radiolarian zonations. The dinocyst biostratigraphic scheme includes five biozones and four major boundaries. A first stratigraphic boundary, at 4.4 Ma, is associated with a change in productivity. The other boundaries, at 2.7 Ma, 1.7 Ma, and 0.7 Ma, correspond to the onset of the modern halocline, an intensified cooling period, and the end of the Mid-Pleistocene Transition respectively. Moreover, the analyses of dinocyst assemblages illustrate long-term changes in the surface ocean after 5.3 Ma. The occurrence of Ataxiodinium zevenboomii, Impagidinium velorum, and Impagidinium patulum suggests warm-temperate conditions until approximately 4.2 Ma. Between 4.2 and 2.7 Ma, colder and less saline events marked by an increase in cold-tolerant species, such as Habibacysta tectata, suggest regional cooling and/or lower salinity of surface water, which might be related to Alaskan glacier meltwater discharges. From 2.7 to 1.2 Ma, the presence of Impagidinium pallidum and cysts of Pentapharsodinium dalei suggests low-salinity, cold, and stratified surface waters, whereas major drops in dinocyst fluxes are linked to a decrease in productivity and harsh conditions. Progressive change from cold, stratified waters to warmer and saltier conditions occurred between 1.2 and 0.7 Ma during the Mid-Pleistocene Transition. After 0.7 Ma, dinocyst assemblages are characterized by the alternating dominance of Brigantedinium spp. and Operculodinium centrocarpum, suggesting fluctuations between nutrient-rich, low-salinity, cold waters and cool-temperate environments.