This project collects the genomic and transcriptomic data generated for Diplonema japonicum to facilitate genome assembly and annotation as part of the Aquatic Symbiosis Genomics (ASG) Project (https://www.aquaticsymbiosisgenomics.org/) from samples supplied by the ASG Evolution-of-New-Symbioses Hub (https://www.aquaticsymbiosisgenomics.org/collaborators/evolution-of-new-symbioses-in-single-celled-eukaryotes/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).