Analyses of marine palynomorphs, including dinocysts and acritarchs in Pliocene-Pleistocene sediments of the Ocean Drilling Program (ODP) Site 887 in the Gulf of Alaska led to define a biostratigraphical scheme, which we compare to bio-events in the regional diatom and radiolarian zonations. The dinocyst biostratigraphical scheme includes five biozones and four major boundaries. A first stratigraphical limit at 4.4 Ma is associated with a change in productivity, and the other limits at 2.7 Ma and 1.7 Ma and at 0.7 Ma, would respectively correspond to onset of the modern halocline, a cooling intensification and the end of the Mid-Pleistocene transition. 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 about 4.2 Ma. Between 4.2 and 2.7 Ma colder/fresher events marked by an increase of cold-affinity species as Habibacysta tectata suggest regional cooling and/or freshening 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 cyst of Pentapharsodinium dalei suggests fresh, cold and stratified surface waters whereas major drops in fluxes are linked to decrease in productivity and the onset of harsh conditions. Progressive change from cold-stratified waters to warmer and saltier conditions is suggested to occur from dinocyst assemblages between 1.2 and 0.7 Ma during the mid-Pleistocene Transition. After 0.7 Ma, the dinocyst assemblages are characterized by the alternating dominance of Brigantedinium spp. and Operculodinium centrocarpum, thus suggesting fluctuations between nutrient-rich, low saline and cold waters and cool temperate environments.