We have sequenced the 18S rRNA gene of the raphidophyte Heterosigma carterae (Hulburt) F.J.R. Taylor and have performed a detailed molecular phylogenetic analysis of heterokont algae. Maximum likelihood, maximum parsimony and two distance methods (Fitch and neighbor joining) all show that Heterosigma is specifically related to eustigmatophytes and chrysophytes: somewhat more distant are the xanthophytes and brown algae, recently classified together in a superclass Fucistia. Our trees also show that chloroplasts have been lost twice independently in pedinellids. We discuss the phylogeny and nomenclature of heterokont algae (phylum Ochrophyta or Ochrista), and present a revised phylogenetic classification of Ochrophyta down to the level of subclass. We transfer both raphidophytes and eustigmatophytes into the infraphylum Chrysista (which previously comprised only Fucistia and chrysophytes), even though they lack an intraplastid eyespot and associated swelling on the smooth cilium that characterize ...