This study investigated dinoflagellate cyst records spanning the latest Pleistocene to the late Holocene on the Vancouver Island margin, identifying 14 autotrophic and 26 heterotrophic taxa. Four dinoflagellate cyst zones were defined and related to paleoclimatic and paleoceanographic conditions. Zone I (~14–~11.6 cal kyr BP) showed the lowest primary productivity (PP), indicated by the lowest total cyst concentrations, with Brigantedinium spp. dominant in assemblages. This was likely due to cooler conditions associated with glacial meltwater input and/or weak coastal upwelling. Zone II (~11.6–~10.6 cal kyr BP) showed a slight increase in total cyst concentrations, a rapid increase in Operculodinium centrocarpum sensu Wall and Dale 1966 and the highest Nematosphaeropsis labyrinthus abundances. This zone was linked to reduced meltwater input and increased coastal upwelling, promoting primary productivity. Zone III (~11.6–~8.2 cal kyr BP) showed a rapid increase in PP, with total cyst concentrations peaking and autotrophic taxa reaching their highest abundances. This was associated with strengthened California Undercurrent and increased upwelling, coinciding with the highest insolation intensity. The high Impagidinium abundances indicated more open ocean conditions. A sharp increase in Operculodinium centrocarpum-truncate processes during ~9–8.2 cal kyr BP may be related to the 8.2 ka event and decelerated sea-level rise. Zone IV (~8.2–~2.3 cal kyr BP) indicated gentle fluctuations in PP, with an overall total cyst concentrations decline, reaching the lowest around 8.0 cal kyr BP, followed by a slight increase at ~6.5 cal kyr BP, and subsequent stabilization.