The typical dinoflagellate chloroplast contains the carotenoid peridinin, which is bound in a unique water soluble light harvesting protein, the extrinsic peridinin chlorophyll protein. These organisms also use a proteobacterial form II RuBisCO. Nuclear phylogenies based on SSU rRNA show dinoflagellates with and without plastids to be related in a manner which implies that the peridinin plastid may have been acquired early in dinoflagellate evolution and lost multiple times. To determine the origin of the peridinin dinoflagellate plastid we have sequenced the large subunit ribosomal RNA and the psbB gene from the plastids of several dinoflagellates. Unfortunately, because the peridinin plastid seems to lack a large master genome, there is no phylogenetic information available from comparitive gene order or content. Despite the high rate of sequence evolution, sequence analyses are the most promising source of phylogenetic information. Analyses of the LSU sequences group dinoflagellate plastids with the plastids of the nonphotosynthetic parasitic apicomplexans, but the high substitution rate makes these phylogenies suspect. Analyses using the psbB gene indicate that the dinoflagellate plastid is derived from the red algal plastid lineage, with moderate support. The dinoflagellate plastid appears to be a secondary, tertiary (or quaterniary) endosymbiont which has undergone a dramatic series of changes. We present several acquisition scenarios which attempt to explain these data.