The appropriate taxonomic organization of Pleurothallis (subtribe Pleurothallidinae, family Orchidaceae) and its subgenera has been debated for more than a century. Recent phylogenetic studies have suggested that subgenera previously elevated to the level of genus based on morphological studies are most appropriately considered subgenera of Pleurothallis. This study analyzed the hypothetical open reading frame ycf1, a plastid gene, in order first to determine its utility in phylogenetic study at the generic and infrageneric level, and second to test support for the existing models or suggest a new model for taxonomic organization of Pleurothallis. A 1,200 bp 5’ region and a 1,500 bp 3’ region of the ycf1 gene were sequenced for representative species of each of the morphologically-based groups within Pleurothallis sensu lato and phylogenetic trees were generated for each region using maximum-parsimony analysis. The tree generated from the 5’ region exhibited minimal topological structure, suggesting either that the species sequenced are too closely related to be segregated into unique genera or the 5’ region of the gene did not contain enough parsimony informative sites to be useful at this level of study. The 3’ ycf1 gene tree had considerably more topology but the small number of species sequenced limits the conclusions that can be drawn from the phylogenetic tree.