Sri Lanka, a biodiversity hotspot in South Asia, is home to 9–10 species of the genus Piper. Although previous studies have investigated the overall phylogenetics and biogeography of this genus, Sri Lankan species have largely been overlooked. In this study, we employed restriction-site-associated DNA sequencing (RADseq) to explore the phylogenetics, divergence times, and evolutionary relationships of Sri Lankan Piper species. We analyzed 27 Piper accessions, representing endemic, native, and introduced species, yielding 284,013 high-quality single nucleotide polymorphisms.