Abstract Dinoflagellate symbionts of the genus Symbiodinium are integral to the success of the coral holobiont (a coral host and the microbial community it harbours), however despite their importance we currently have a very limited knowledge of the genes which they possess and their genomic organisation. Analysis shows that the number of expressed sequence tags (genes that are expressed) available for Symbiodinium (7964) is less than 1/10 of those available for the scleractinian coral host (103,434). This lack of DNA sequence information limits the functional genomic studies that can be undertaken from the symbiont perspective. In addition these sequences are from only three Symbiodinium types (C3, A1, A3) and do not represent the large diversity of clades and subclades seen. Here we summarise our current understanding of the Symbiodinium genomic content with reference to our knowledge of other dinoflagellates. The genetic information of Symbiodinium is encompassed in the nuclear, plastid and mitochondrial genomes. As is the case with other dinoflagellates these three genomes are significantly different from the “general” phototrophic eukaryote. Firstly the nuclear genome of dinoflagellates is extremely large, utilises modified DNA bases not normally found in eukaryotes, and tandem repeat regions seem to contain the most highly expressed genes. Meanwhile the plastid genome, which normally contains between 40 and 250 genes in other eukaryotes, has been reduced to 18 genes encoded in “minicircles.” Finally the dinoflagellate mitochondrial genome only encodes for 2 or 3 proteins instead of the normal 40–50 in other eukaryotes. While we have some knowledge of Symbiodinium genome structure, little is known about its transcriptome. With the advent of inexpensive high throughput sequencing technologies, our understanding of the Symbiodinium genome will rapidly increase and we will begin to be able to look into the responses of these important single celled organisms.