This dataset contains the combined molecular matrix used for phylogenetic analyses of the tribe Coreopsideae (Asteraceae), with emphasis on the genera Dahlia, Dicranocarpus, Hidalgoa, Henricksonia, Heterosperma, and Electranthera. The matrix includes Sanger sequences (cpDNA and nrDNA) and DArTseq-derived SNP markers, which together were used to infer phylogenetic relationships and to map morphological character evolution across the group. The file is provided in NEXUS format and includes the concatenated alignment used in the phylogenetic analyses presented in the associated publication. Voucher information and GenBank accession numbers are available in the supplementary materials of the article.