The genome of the pufferfish, Fugu rubripes (Fugu) is compact. With a similar gene complement to mammals and a genome size of just 400 Mb, gene density is high averaging one every 6-7 kb. Initial characterization of this genome has shown that although genes are much smaller and more densely spaced, their intron/exon structure is conserved with the resulting introns being small. There is little repetitive DNA in the genome and this greatly facilitates comparative genomic studies. The coding content of genes is highly conserved as are critical regulatory elements of some genes. Other DNA is not, however, and this allows the identification of homologous coding sequence between Fugu and mammalian genes. Although the genome of Fugu is 7.5 times smaller than the human genome, not all genes are reduced proportionately. Some regions of the genome show conserved synteny with mammalian genomes, although at the present time only short physical distances have been examined. The structure of the genome is also being studied. Initial data suggest that this may be different to that found in mammals. It is not clear that the same kind of isochore structure is present in this early vertebrate genome. Patterns of methylation may be different resulting in a different distribution of CpG islands. An attempt is being made to centralize both resources and data from the genome of Fugu so that everything may be integrated into a single, publicly accessible database which in turn, may be integrated with databases from other organisms.