Background The whale shark forms an interesting subject for a genome project because it represents a phenotypic extreme: the largest body size of any piscine vertebrate. Sharks are also important comparative genomics subjects because they were the first vertebrate lineage to evolve and adaptive immune response. To date, however, no shark has had its complete nuclear genome sequenced and assembled. Approach Sequencing and assembly of the whale shark genome has been underway for almost 6 years, based on tissue samples from animals in the collection at Georgia Aquarium. Initial efforts focused on 454 pyrosequencing, and later Illumina sequencing. The most recent assembly has incorporated longer-read sequence data acquired using Pacific BioSciences technology. For the genome assembly we used a de novo approach. Results We estimate the total whale shark genome size at 3.44 Gbp, 3.5x larger than that of the closest related species for which whole genome data exist, the holocephalan Callorhinchus milii (950 Mbp). The mitochondrial genome is of fundamentally similar structure to that of other elasmobranchs and whole mitogenome phylogeny affirms the accepted phylogenetic placement of this species among the Orectolobiformes. Conclusions The availability of the whale shark genome will facilitate detailed investigations of global population structure that are a necessary precursor to effective conservation management. Moreover, whale shark genome sequence should find use in comparative studies of evolution, immunology and metabolism. Those interested in collaborating on such studies should contact the authors.