The Subtropical Convergence Zone (SCZ) in the Chatham Rise region east of New Zealand supports productive fisheries and benthic ecosystems and is an important CO2 sink. The SCZ trophic system is underpinned by a microbially-dominated food web, requiring an efficient link between pico-sized producers and larger consumers to support the necessary trophic transfers. However, the role of mesozooplankton (>200 μm body size) as intermediaries in this trophic transfer is not well understood. This study investigated the trophic role of mesozooplankton in subantarctic (SA) and subtropical (ST) waters of the SCZ, south and north of the Chatham Rise, in summer 2000. Mean summer biomasses of mesozooplankton were low in SA and ST waters (181 and 137 mg dry weight m−2, respectively) relative to other seasons. Mesozooplankton biomass was dominated by copepod nauplii, copepodites and small adults (Oithona, Calocalanus, Clausocalanus) and pre-adult euphausiids, while pelagic tunicates (salps and pyrosomes) were rare. Copepod gut pigment contents showed high weight-specific phytoplankton grazing, and feeding incubations showed rapid consumption of ciliates by all sizes of copepods, indicating omnivory as an important trophic mode. Irrespective, consumption by mesozooplankton had only minor impacts on water column phytoplankton and microzooplankton biomass, and production, and nutrient regeneration. Linear Inverse Ecosystem Models (LIEMs) were used to investigate the overall role of mesozooplankton in carbon (C) cycling among autotrophs, heterotrophs, and export fluxes, based on measured plankton rates and biomasses from summer 2000 in SA and ST waters. LIEMs indicated a dominant role for protistan zooplankton (ciliates and heterotrophic nanoflagellates) in consumption of primary biomass and production (71–97%) and a strong protistan – mesozooplankton trophic link. The summer mesozooplankton were shown to be important in transferring energy from the microbially-dominated food web to sinking fluxes and to higher trophic levels (~12 mg C m−2 d−1 to each), the latter equivalent to ~0.42 of mesozooplankton C consumed by higher trophic levels annually in the Chatham Rise SCZ.