A phylogenetic analysis of five coding and noncoding chloroplast loci, totaling 6.6 kb of aligned nucleotide and indel characters, suggests that the large neotropical bamboo genus Chusquea is embedded within the much smaller Andean genus Neurolepis. Monophyly of each taxon was anticipated due to the unique occurrence of dimorphic multiple buds in Chusquea and the lack of aerial branching in Neurolepis. We tested whether the unexpected placement of Chusquea might be the result of a biased analysis. Both Neurolepis and the outgroup taxa have long branches that could influence rooting and inferred ingroup relationships. A number of methods were employed to test for long-branch attraction and sampling effects in our topology. Alternative hypothesis testing using a conservative form of the Shimodaira-Hasegawa test indicated that paraphyly of Neurolepis is a significantly better explanation of the data than monophyly, even when models of character evolution are changed. Given the robustness of the topology, high support measures for clades on the tree, and the results of the Shimodaira-Hasegawa tests, we conclude that chloroplast genomes indicate probable paraphyly of Neurolepis with respect to Chusquea. The species of Neurolepis are therefore transferred to Chusquea, resulting in the following new combinations and names: Chusquea acuminatissima, C. angusta, C. asymmetrica, C. cylindrica, C. diversiglumis, C. elata, C. fimbriligulata, C. laegaardii, C. magnifolia, C. mollis, C. nana, C. nobilis, C. petiolata, C. rigida, C. silverstonei, C. spectabilis, C. steyermarkii, C. stuebelii, C. tovari and C. villosa. The names Neurolepis elata, N. stuebelii, N. weberbaueri, Planotia ingens, and P. tessellata are lectotypified.