Among the least studied clade of velvet worms (Onychophora) is a clade of Neotropical Peripatidae (=Neopatida). Neopatida has been traditionally divided into an Andicoles group and a Caraïbes group, which now correspond to Oroperipatus and the remaining genera, respectively. Panama is located in a unique position bridging the faunas of both clades and of two large continents, both of which host an important diversity of velvet worms, yet taxonomic study of the Panamanian onychophorans has been largely neglected. In this study we critically evaluate the onychophoran diversity of Panama, redescribe a species from the former Canal Zone and describe a new species from the Pacific side, close to Costa Rica, as Epiperipatus bernali sp. nov., with a unique combination of characters visible under the SEM. We further discuss the existence of multiple lineages of Onychophora in Panama, both from the Andicoles and Caraïbes groups, and within the latter, with connections to different lineages, both from South and Central America.