Observational and modelling studies have shown that currents along the east coast boundary of Tasmania are influenced by the strength of a residual East Australian current (EAC), experiencing distinctive seasonal and interannual variation in water properties. In this study we investigated whether the influence of the EAC changes the microbial community structure, including photoheterotrophic Proteorhodopsin-containing Bacteria and Archaea (PRBA), a key component of the microbial community. Seawater samples were collected from August 2011 to March 2012 from surface waters at the National Reference Station Maria Island Mooring. The microbial communities were characterized by 454 pyrosequencing of the 16S rRNA and proteorhodopsin genes. Our data show marked changes in microbial assemblages over the season, in particular in February and March, when the maximal effect of the EAC was observed by the increased abundance of Synechococcus, Prochlorococcus and Pelagibacteraceae associated with warm and highly oligotrophic open ocean waters. PRBA sequence diversity indicated that Alphaproteobacteria related clades SAR116 and SAR11 predominated in spring and summer while Archaea marine group IIb predominated mostly in winter. Quantitative PCR demonstrated that SAR 11 PRB populations were more abundant during the last months of summer and linked to high salinity and temperature and low nutrient concentrations (NO2-/NO3- and PO43-). Overall, these findings indicate that further increases in the influence of the EAC could alter the bacterioplankton community structure towards that of typical of open ocean systems.