DNA sequence data generation has traditionally been a significant bottleneck in the production of well-resolved molecular phylogenies both in terms of time and money. As smaller laboratories now have access to molecular techniques once accessible only in large laboratories with expensive equipment, and the cost per base of DNA sequencing has dramatically dropped, most laboratories, including those working on nonmodel organisms, can produce large molecular datasets. In this study, we discuss the technical and financial details of producing a reduced-representation genomic dataset for the resolution of species-level phylogenies of two distantly related ant genera (Cephalotes and Polyrhachis), and then compare our resulting phylogenies with phylogenies generated by previous studies using the more traditional gene-based approach. We demonstrate that genotyping-by-sequencing is a cost-effective and appropriate method for species-level and potentially higher phylogenetics in insects but recognize that bioinformatic skills will now be the bottleneck for many laboratories and researchers.