The oceans sequester 31% of atmospheric carbon annually 1, but the magnitude of biologically enhanced sequestration is not evenly distributed across the globe 2. Measuring surface primary productivity offers a reasonable proxy for estimating carbon flux into the ocean 3 but entirely misses the processes that affect carbon export to sequestration depths. A high proportion of carbon flux is broken up 4 or respired 5 by organisms at mesopelagic depths (200-1000 m). At low and mid-latitudes, daytime biomass peaks of mesopelagic organisms are clearly present and detectable as sound-scattering layers, and up to 40% of oceanic carbon passes through these layers 6,7. Here we demonstrate that acoustic backscatter, a proxy for abundance of mesopelagic fish and zooplankton decreases by up to 97% across polar fronts, revealing a distinct pelagic structure in high latitude systems. As mesopelagic fish and macrozooplankton comprise a large component of active carbon transport in the upper ocean, this latitudinal reduction in mesopelagic biomass across thermal fronts, in both the Arctic and Antarctic, suggests different carbon flux attenuation schemes exists in ocean twilight zones of polar ecosystem compared to low latitude systems. Rapid ocean warming projected at mesopelagic depths8 will likely disrupt vertical connectivity and alter biogeochemical cycles at high latitudes.