Piper (Piperaceae) is a species-rich pantropical genus (∼2000 species) with distinctive morphological characteristics such as swollen nodes, lack of a perianth, and one-seeded berry fruits. Sub-generic lineages within Piper are often associated with morphological traits and are well supported with molecular data, but sampling in previous studies was incomplete and conflict exists between morphological data and molecular inference. In this paper, Piper section Enckea is evaluated for monophyly by pairing DNA, primarily from herbarium material, with the Angiosperms353 bait set, high throughput sequencing, recently developed bioinformatic techniques, and two methods of phylogenetic reconstruction, maximum likelihood and multi-species coalescence. The results suggest continued support for recognition of Piper sect. Enckea as a monophyletic section and contribute to a better understanding of relationships among species within the section. However, they also raise questions about the morphological features used to define P. sect. Enckea and delimit species within the section.