This dataset includes the de novo genome assembly and annotation for the Mariana Crow/Åga (Corvus kubaryi) described in Cortes-Rodriguez et al. 2019. Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi). Genes. 10(3), 187. The whole genome shotgun data have been published in the NCBI SRA under accession SRX4386043 and duplicated in the ENA under accession ERX3480537.