Diet analysis is an important tool in conservation biology, where it can provide information on species’ resource use and habitat requirements. Environmental DNA (eDNA) is a valuable source for diet reconstruction, but the use of reference databases comprising short DNA sequence markers can limit the resolution for accurate species identification. We explore how the optimal use of emerging complete organelle DNA reference databases such as PhyloNorway, may lead to better taxonomic identification of plants in animal diet. We collected faecal samples from eight individual western
capercaillies located in Norway. We used shotgun sequencing to obtain 150bp paired reads and diet information was retrieved by blasting to both GenBank and the PhyloNorway reference database. Our preliminary results suggest that when using PhyloNorway as a reference database, we were able to retrieve at least 160 times more reads assigned to the species-level.