Photosynthetic dinoflagellates, Symbiodiniaceae, live together with many marine organisms of coral reefs and are currently classified into fifteen groups. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, that have been detected in corals, have been reported. However, genomes of Durusdinium that are well known for thermal tolerance (found in corals resistant to bleaching phenomena) are not accessible. To explore the genetic background of the coral symbiont, Durusdinium, here, we sequence, assemble, and annotate the genome of Durusdinium trenchii from the coral Favia speciosa in Okinawa, Japan. This work will provide a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.