In the present study we examine factors that affect the downward flux of biogenic carbon in the NE subarctic Pacific, one of the important high-nutrient-low-chlorophyll (HNLC) regions in the open ocean. We focus on the role of mesozooplankton, since their seasonal peaks in biomass and growth are in phase with the seasonal variations in the downward POC fluxes, whereas phytoplankton biomass is more-or-less uniform year-round. The relative importance of mesozooplankton and algal sinking was examined using the pigment composition of material accumulated in short-term free-drifting sediment traps positioned just below the upper stratified surface layer (ca. 100–200 m). This was compared with the phytoplankton composition in the surface waters, and with the grazing activity (gut pigments and fecal pellet production rates) of the most abundant large copepods. We also examined whether the relationships between the downward flux of carbon and pelagic processes were similar in the coastal, continental margin and offshore HNLC regions of the NE subarctic Pacific, the latter represented by Ocean Station Papa (OSP). Our results show that grazing had a variable impact on the downward flux of biogenic carbon. Carbon-transformed pheopigments (particularly pyropheophorbide a, frequently associated with copepod grazing) represented up to 13% of the total downward POC flux inshore (in May 1996) and 8–9% at OSP in May and February 1996, respectively. This flux of pheopigments was accompanied by a large potential input of fecal pellets from large copepods (as estimated from defecation rates of freshly collected animals) only in May 1996 at OSP, suggesting that pheopigments came from other sources (other herbivores, senescing algae) in February. The larger flux of pheopigments in May was probably related to the abundance of mesozooplankton at that time of the year. During summer (August 1996), both the flux of pheopigments and the potential input of fecal pellets from large copepods were negligible at OSP, consistent with more intense pelagic recycling reported in other studies. Inshore, the flux of carbon-transformed pheopigments was slightly higher than at OSP, and its contribution to the downward POC flux in May 1996 was twice that in August 1996. In contrast, the potential input of feces carbon was higher in August than in May 1996, again suggesting other sources for pheopigments found in the traps. The contribution of sinking phytoplankton to the downward biogenic flux was negligible in summer, when prymnesiophytes (indicated by the presence of 19′-hexanoyloxyfucoxanthin) and pelagophytes (19′-butanoyloxyfucoxanthin-containing) dominated in surface offshore waters. The contribution of sinking algae was maximal (9%) in winter (February 1996) at OSP, when fucoxanthin (mainly a diatom marker) dominated the carotenoid composition in the traps and when the abundance of diatoms in surface waters showed its seasonal maximum for this station. Inshore, the low contribution of diatoms (fucoxanthin) to the sinking fluxes may have resulted from inadequate sampling (i.e. the spring bloom may have been missed). Overall, we conclude that: (a) large copepods significantly influenced the downward POC flux only during spring at OSP; (b) unidentified herbivores (e.g. salps, pteropods) producing pigmented, fast-sinking fecal material likely had an important impact during winter; (c) algal sinking made a small contribution to the downward POC flux (maximum in winter); and (d) neither algal sinking nor mesozooplankton grazing had a significant influence on the downward flux of biogenic material in summer at OSP.