Next-generation sequencing (NGS) is enabling plant systematists to capture orders of magnitude more sequence data for phylogenetic studies. As systematists grapple with how to best apply NGS to their taxa of interest, a deluge of review papers, methods, and analytic tools makes choosing the right method difficult. Oreocarya, a genus of 63 species in the Boraginaceae, is a good example of a group with few genomic resources and a lack of species-level resolution. Traditional methods, using PCR and Sanger sequencing of a few molecular markers, have failed to resolve species-level relationships. To test the utility of using NGS genome skimming for systematic studies within Oreocarya, 100-bp single-end Illumina reads were generated for 20 taxa (including two outgroups) in half of an Illumina HiSeq 2000 lane, resulting in 1.7-9 million reads per sample. A combination of de novo and reference-guided assemblies were used to recover the nuclear ribosomal cistron, the plastome, and nine mitochondrial genes; these data were used to infer phylogenies using Maximum Likelihood, Bayesian Inference and species-tree methods. Additionally, NGS data were used to inform future studies in Oreocarya, by identifying published conserved single-copy orthologous low-copy nuclear genes (LCNG), and calculating multiplexing levels. Although genome skimming provides a much-improved primary data collection method for phylogenetic resolution at the species level, and is suitable for systematic revision of Oreocarya at the sectional level; targeting of LCNG holds the most promise for a well-resolved phylogeny of Oreocarya in the future.