Most species belonging to the toxigenic genus Dinophysis have chloroplasts of cryptophyte origin. Whether these chloroplasts are temporarily sequestered from the prey, or permanently established under the control of the dinoflagellate is currently disputed. To investigate this, a culture of Dinophysis acuminata was established by feeding it the phototrophic ciliate Mesodinium rubrum (= Myrionecta rubra), which again was fed the cryptophyte Teleaulax amphioxeia. Molecular analysis comprising the nucleomorph LSU and two chloroplast markers (tufA gene and a fragment from the end of 16S rDNA to the beginning of 23S rDNA) resulted in identical sequences for the three organisms. Yet, transmission electron microscopy of the three organisms revealed that several chloroplast features separated D. acuminata from both T. amphioxeia and M. rubrum. The thylakoid arrangement, the number of membranes around the chloroplast as well as the position and the arrangement of the pyrenoids were strikingly different. Considering both molecular and ultrastructural evidence, our data indicated that the chloroplasts in D. acuminata are permanent chloroplasts originating within Teleaulax or another closely related cryptophyte genus. Electron microscopy also provided new information on the peduncle of D. acuminata, which is used in food uptake.