Primers from a recently published study that identified a set of low-copy nuclear genes (LCNG) in multiple angiosperms were used to obtain sequence data from three LCNG (Chlp, Agt1, and Hmgs) for phylogenetic inference at the species level. The phylogenetic utility of each of these markers was compared to ITS and seven chloroplast loci (trnL, trnG-S, ycf5, accD, rpoC1, trnK intron, psbM-trnD intergenic spacer) widely used in phylogenetic analyses. Here we use Valerianaceae as an example for two reasons: 1) the group has a well-supported “backbone” phylogeny based on numerous molecular markers; and 2) there are several species groups (e.g. the South American taxa) that have been particularly difficult to resolve, potentially due to a rapid or recent radiation. Although these new markers added nucleotide characters, they did not provide significant phylogenetic information to resolve relationships among closely related species of Valerianaceae. Likewise, relationships among some of the major clades of Valerianaceae are still not resolved with much certainty. This study indicates that several of these nuclear markers provide a significant increase in phylogenetic signal compared to traditional chloroplast markers, but information content within these regions is most useful at broader-scale phylogenetic levels. Advances in “next-generation” sequencing technologies may ultimately make their utility obsolete.