The genome project of Hydra viridissima strain A99 H. viridissima is the most basal species in the genus Hydra, and a symbiotic species that establishes a mutualistic relationship with microalgae Chlorella. We also reported the genome of its specific symbiotic algae, Chlorella sp. A99 . Genome sequence of H. viridissima A99 was reconstructed by shotgun approach using Illumina pair-end and mate-pair libraries with ~90x total coverage. The genome assembly is 284 Mbp long and consists of 2,677 scaffolds with N50=1.1 Mbp. The genome was estimated to contain 21,476 protein-coding genes. The BUSCO method supports 84% and 91% of the gene models as complete and as partial sequences, respectively. This whole-genome shotgun sequencing project has been deposited at DDBJ/ENA/GenBank under the accession QPEY00000000 (BioProject ID: SAMN09635813 ). RNA-seq reads has been deposited at SRA of NCBI (SRX6792700-SRX6792705 ).