The transport of microalgae in the ballast tanks of shipping vessels is of global concern because many algal species can survive in ballast tanks as nonmotile or cyst stages increasing the likelihood of introductions into foreign ports. In 2004 a peridinoid dinoflagellate was collected and isolated from ballast residuals of the merchant vessel Southern Fighter in Port Tampa Bay, Florida, USA. Light and electron microscopy of the motile and nonmotile peridinoid cells indicated the dinoflagellate was Vulcanodinium rugosum. Bayesian and maximum-parsimony (MP) phylogenetic analyses of V. rugosum strain CCFWC516 showed that sequenced regions of its LSU and ITS matched those of V. rugosum strains from Japan but were divergent from those strains from New Zealand and France. LC–MS analyses indicated that strain CCFWC516 did not produce the neurotoxin pinnatoxin, an ability that has been reported for other strains of this species. Analyses did show, however, that strain CCFWC516 did produce portimine, a cyclic imine produced by all other strains of this species. The M/V Southern Fighter visited numerous ports along the coast of Japan and the North Sea before sailing to Florida. The phylogenetic match to Japanese strains, as well as the ship's ballast exchange history, suggests that strain CCFWC516 originated from Japan. In light of the increase in global shipping traffic, increases in vessel size and capacity, and the increased connectivity between the Pacific Ocean and the Caribbean and Gulf of Mexico that will result from the widening of the Panama Canal, the introduction of nonnative, harmful algal species is an area of heightened concern and calls for increased vigilance.