The included files are the alignments of DNA or amino acid sequences used for phylogenetic analyses of Auchenorrhyncha (Insecta: Hemiptera) in the manuscript by Bin et al. submitted to the journal “Systematic Entomology.” The files are plain text in either FASTA (.fa or .fas suffix) or PHYLIP (.phy suffix) format. Matrix0 is the set of all loci after multiple sequence alignment and trimming (hereafter called). Matrix1 consists of loci having 75% average bootstrap support and 80% taxon completeness (hereafter called Matrix1). Matrix2 consists of loci having 75% average bootstrap support and 95% completeness. Matrix2_nt12 is the same as Matrix2 but with third codon positions excluded. More details on how the datasets were compiled is provided in the Methods section of the manuscript file, also included as a PDF. Supplemental figures for the submitted manuscript are also provided as a PDF for additional information.