The Baylor College of Medicine recently sequenced and annotated the Hyalella azteca genome as part of the i5k pilot project. The Hyalella azteca research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. This dataset presents the Hyalella azteca genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource. The corresponding genome assembly in NCBI is GCA_000764305.1.