Diatom and dinoflagellate species that are not endemic to a region can be inadvertently introduced when their resistant resting stages are discharged with the ballast-tank waters and sediments of bulk cargo vessels. A survey of 343 cargo vessels entering 18 Australian ports showed that 65% of ships were carrying significant amounts of sediment on the bottom of their ballast tanks. All of these samples contained diatoms, including species that are not endemic to Australian waters. Diatom resting spores, especially of Chaetoceros, were also detected. Dinoflagellate resting spores (cysts) were present in 50% of the sediment samples. Of the 53 cyst species identified, 20 (including Diplopelta, Diplopsalopsis, Gonyaulax, Polykrikos, Protoperidinium, Scrippsiella and Zygabikodinium spp.) were successfully germinated to produce viable cultures. Such diversity of diatom and dinoflagellate species in ships' ballast water suggests that the apparent cosmopolitanism of many coastal phytoplankton species may be due partly to the global transport of seawater ballast. Of considerable concern was the detection in 16 ships of cysts of the toxic dinoflagellates Alexandrium catenella, Alexandrium tamarense and Gymnodinium catenatum. One single ballast tank was estimated to contain >300 million viable A.tamarense cysts, some of which were successfully germinated in the laboratory to produce toxic cultures. These toxic dinoflagellate species, which can contaminate shellfish with paralytic shellfish poisons, pose a serious threat to human health and the aquaculture industry. Ballast-water quarantine measures recently introduced in Australia are discussed. Mid-ocean exchange of ballast water is only partially effective in removing dinoflagellate cysts which have settled to the bottom of ballast tanks. The present work indicates that the most effective measure to prevent the spreading of toxic dinoflagellate cysts via ships' ballast water would be to avoid taking on ballast water during dinoflagellate blooms in the water column of the world's ports.