Two discontinuous sediment trap records of organic-walled dinoflagellate cyst (dinocyst) flux, each sampling > 300 days within the years 2005–2009, were derived from two time-incremental traps deployed at 1500 m water depth east of New Zealand. The traps sampled flux from beneath two distinct surface water masses on either side of the Subtropical Front: (i) warm, seasonally macronutrient-depleted Subtropical and (ii) cold, micronutrient-limited Subantarctic waters. Nineteen dinocyst taxa or taxonomic groups were identified from the trap samples. Trap assemblages at both sites were dominated by cysts of Protoperidiniaceae, notably Brigantedinium spp., which comprised almost ~ 98% of the dinocyst flux. The seasonality of the dinocyst flux differed between the traps, with a pronounced spring flux in the Subtropical trap, while seasonal variation in the Subantarctic trap was relatively muted. In Subtropical waters, moderate correlation was observed between Protoperidiniaceae cyst flux and chlorophyll a concentrations in surface waters in the 3–4 weeks prior to sampling. In Subantarctic waters, there was a weak correlation between Protoperidiniaceae cyst flux and reduced intensity of storm-induced turbulence during the preceding 2–3 weeks. There was a large discrepancy between dinocyst assemblages in the traps and those observed in nearby sea-floor sediments. Protoperidiniaceae dinocysts, particularly Echinidinium and Brigantedinium, were highly under-represented in the sea-floor assemblages. These forms are more susceptible to degradation in oxygenated sediments than other dinocysts, but inter-annual variability in cyst flux, or short-term variation not covered by sampling discontinuities in the current study could also have contributed to this discrepancy. The major differences in the seasonality of dinocyst fluxes between the two water masses examined in this initial study, suggest that mean-annual rather than seasonal climatologies are more appropriate for dinocyst-based quantitative palaeoenvironmental reconstructions in the New Zealand region.