Pleurothallis is the largest myophilous (fly-pollinated) genus in subtribe Pleurothallidinae. Although many studies show highly specific relationships in pollination systems in the Orchidaceae, our understanding of these relationships in myophilous orchids is almost non-existent (Borba & Semir 2001). This study focuses on the floral micromorphology, specifically the lip and column, of species within subgenera Ancipitia and Scopula. Scanning electron microscopy of the micromorphology of floral structure shows a range of morphology and pollination mechanisms within the two studied subgenera. These include deceit pollination by pseudocopulation and reward pollination. In concert, phylogenetic analysis was performed to determine if a correlation existed between morphology or pollination mechanism and taxonomic groupings. Maximum parsimony trees were produced using ITS and matK sequences for subgenera Ancipitia, Scopula, and Pleurothallis, with species from the genera Laelia, Pabstiella, and Arpophyllum as outgroups. The ITS, matK and combined trees strongly support an Ancipitia/Scopula section within a monophyletic subgenus Pleurothallis. Within this section, both reward and deceit pollination mechanisms are found, meaning they are not restricted to the current taxonomic groupings. Morphological and genetic data therefore support the grouping of subgenera Ancipitia, Scopula, and Pleurothallis into one monophyletic subgenus.