The delimitation of species boundaries is a question that has plagued biologists, taxonomists, and philosophers alike. Subtle and minor morphological differences in a widespread species complex makes delimiting the boundaries of the species particularly challenging. High throughput targeted sequencing of hundreds of loci has allowed researchers to gain better insight to phylogenetic processes and gain confidence in previously ambiguous relationships. Piper amalago sensu lato occurs throughout the Neotropics.  Piper amalago is morphologically similar to many other Neotropical Piper species that have more restricted ranges or occur as narrow endemics.  Taxonomists have debated whether the morphological differences between Piper amalago and other similar species are significant.  Recent data indicates that other Neotropical Piper species are nested within the Piper amalago lineage. Using herbarium specimens of Piper amalago collected throughout its range, specimens of synonyms of Piper amalago and specimens of morphologically similar species, this study focuses on the phylogenetic relationships of Piper amalago and similar species and seeks to determine if Piper amalago forms an exclusive monophyletic lineage that includes other currently recognized species of Piper following the genealogical species concept.  Alternatively, Piper amalago may be better split into a series of species each monophyletic and exclusive.  For this study, the Angiosperms353 bait set is used to retrieve nuclear genes used for building maximum likelihood and multispecies coalescent phylogenetic models.  This analysis will lead to a better understanding of morphological variation within the Piper amalago lineage and where species boundaries should be drawn. The delimitation of species boundaries is a question that has plagued biologists, taxonomists, and philosophers alike. Subtle and minor morphological differences in a widespread species complex makes delimiting the boundaries of the species particularly challenging. High throughput targeted sequencing of hundreds of loci has allowed researchers to gain better insight to phylogenetic processes and gain confidence in previously ambiguous relationships. Piper amalago sensu lato occurs throughout the Neotropics.  Piper amalago is morphologically similar to many other Neotropical Piper species that have more restricted ranges or occur as narrow endemics.  Taxonomists have debated whether the morphological differences between Piper amalago and other similar species are significant.  Recent data indicates that other Neotropical Piper species are nested within the Piper amalago lineage. Using herbarium specimens of Piper amalago collected throughout its range, specimens of synonyms of Piper amalago and specimens of morphologically similar species, this study focuses on the phylogenetic relationships of Piper amalago and similar species and seeks to determine if Piper amalago forms an exclusive monophyletic lineage that includes other currently recognized species of Piper following the genealogical species concept.  Alternatively, Piper amalago may be better split into a series of species each monophyletic and exclusive.  For this study, the Angiosperms353 bait set is used to retrieve nuclear genes used for building maximum likelihood and multispecies coalescent phylogenetic models.  This analysis will lead to a better understanding of morphological variation within the Piper amalago lineage and where species boundaries should be drawn.