Parasitic dinoflagellates of the genus Amoebophrya play important roles in the ecology of estuaries and open ocean environments. Little is known of the cell and molecular biology of Amoebophrya, but the genus is intermediate on phylogenetic trees between apicomplexans and typical dinophycean dinoflagellates. Here, we constructed four cDNA libraries, from different stages after infecting the host, Karlodinium veneficum, with Amoebophrya sp. These libraries were used to generate 898 expressed sequence tags (ESTs), with sequences attributed to either the host or parasite, based on AT bias, codon usage, and occurrence during infection. Overall, 209 sequences were attributable to the parasite and 685 to the host. The 50 putative parasite sequences with good protein matches in GenBank were used to find the same protein from host ESTs. For 26 genes, both host and parasite sequences were identified, of which 20 encoded ribosomal proteins. PCR for seven predicted parasite and two host genes were used to confirm attributions. The most common host and parasite ESTs were compared to see if multiple gene copies were present. The host plastocyanin gene had multiple sequence variants, but parasite rps27a contained only one polymorphism, likely due to an amplification error. Amplification, cloning, and sequencing of five parasite protein-coding genes suggested that the parasite has a single sequence for each gene, but three host genes were found to have multiple variants. The genome of Amoebophrya sp. infecting K. veneficum appears to have an organization more similar to other eukaryotes than to the tandem gene arrangements found in dinoflagellates.