In May 2006 (Austral autumn) the distribution and abundance of the cyanobacteria Synechococcus spp. and Prochlorococcus spp. were examined to assess the connectivity of a forming warm-core mesoscale eddy with the Leeuwin Current and shelf waters off south-west Western Australia. Distributions of the cyanobacteria resulted in two broad categories of samples, those dominated by Prochlorococcus spp. from subtropical and Leeuwin Current waters and those with mixed populations from shelf and eddy waters. Water temperature (21.45°C), salinity (35.46) and nitrate (0.33 μM) contributed to these groupings. Synechococcus spp. reached an integrated abundance of 3.3 × 108 cellscm-2 in warm shelf waters, with 60% of cells in G2 phase in the mid-afternoon (~16:00 hours). Cooler, nitrate-poor oceanic waters were almost exclusively inhabited by Prochlorococcus spp., with the highest abundance of 4.2 × 108 cellscm-2 in cool deep waters off the Capes in the south with 40% of cells in G2 phase in the evening (~19:00 hours). The eddy perimeter represented a clear boundary for both species, but showed connectivity between the shelf and eddy centre as both locations had a mixed community, dominated by Synechococcus spp. Eddies of the Leeuwin Current advect shelf waters, and their assemblages and productivity offshore. © CSIRO 2013.