The Huon Estuary in Tasmania, Australia, flows unregulated through a predominantly native forest catchment. The river has high levels of humics and tannins and contains approximately 15 small aquaculture farms. Over fifty bacterial colonies with differing morphologies were isolated on marine agar from the river and its sediments.The cell free media of six of the bacteria had a powerful lytic effect on the toxic dinoflagellate Gymnodinium catenatum, an introduced species which blooms intermittently in the estuary causing shellfish farm closures. Two of the bacteria were identified, based on molecular and phenotypic analyses, as novel Pseudoalteromonas species. The remaining algicidal bacteria were identified as Cytophaga, Flavobacterium and Bacillis species. Thirty eight strains of Antarctic seaice bacteria were also tested none of which showed any permanent effect on Gymnodinium catenatum. Tests on other algal species were also carried out. The six estuarine bacterial species had no effect on rotifer and diatom species tested. Fatty acid profiles of the fifty bacterial strains and field samples and plate counts reflected great variability indicating the bacterial diversity present in the estuary. This investigation supports the concept that bacteria can play an aggressive role in the microbial food chain. We believe that the potential to use these novel bacteria as agents against toxic bloom-forming microalgae and in other endeavours, will be an area for future research opportunities.