This project collects the genomic and transcriptomic data generated for Phoxinus phoxinus, common name Eurasian minnow, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).