Species within the dinoflagellate genusDinophysiscan produce okadiac acid and dinophysistoxins leading to diarrhetic shellfish poisoning. Since the first report ofD. ovumfrom the Gulf of Mexico in 2008, reports of otherDinophysisspecies across US have increased. Members of theD. cf.acuminatacomplex (D. acuminata,D. acuta,D. ovum,D. sacculus) are difficult to differentiate due to their morphological similarities.Dinophysisfeeds on and steals the chloroplasts from the ciliate,Mesodinium rubrum, which in turn has fed on and captured the chloroplasts of its prey, the cryptophyteTeleaulax amphioxeia. The objective of this study was to generatede novotranscriptomes for new isolates of these mixotrophic organisms. The transcriptomes obtained will serve as a reference for future experiments to assess the effect of different abiotic and biotic conditions and will also provide a useful resource for screening potential marker genes to differentiate among the closely related species within theD. cf.acuminata-complex. The complete comprehensive detailed workflow and links to obtain the transcriptome data are provided.