The Atlantic Meridional Transect (AMT), sampling between 50°N and 50°S, is a trans-oceanic research programme to characterize plankton community structure, productivity and bio-optical properties of the upper ocean in relation to ocean provinces and meso-scale features. As part of a suite of continuous measurements, an optical plankton counter (OPC) has been used on the AMT to characterize the surface distribution of zooplankton based on their abundance and community size structure. Results from the OPC were available in real time, and were subsequently validated against microscope counts of zooplankton sampled concurrently along the AMT. Zooplankton community size structure from two sections of the Transect are presented: from the northern edge of upwelling off West Africa to the UK shelf and between the Falkland Islands and Uruguay, where the Transect traversed a warm core ring. Results showing the zooplankton community size structure together with statistical analysis, using principal component analysis (PCA), are compared with the dynamic oceanographic characteristics along the Transect. The application of the OPC for such basin-scale studies provides a methodology for obtaining data on zooplankton abundance and community structure at the appropriate spatial scales for global-scale modelling of the marine ecosystem.