The forests of the Chocó Region are among the most diverse in the world, however they are under imminent threat of significant degradation. This study uses species diversity and phylogenetic data in the plant genus Piper to select areas of maximum biological diversity to be considered as conservation priorities. Species distributions were obtained from herbarium collections and the literature. A molecular phylogeny based on nucleotide sequence data from the ITS region of the nuclear genome was used to estimate phylogenetic diversity indices. Three diversity indices were estimated: total species richness, number of endemic species, and phylogenetic diversity. Area selection was conducted by maximizing the total value for these indices and also by complementarity. Four regions were selected as the highest conservation priorities: the vicinity of Buenaventura, the Rio San Juan watershed (south of Quibdó), the department of Nariño, and the Rio Atrato watershed. All of them had the highest rankings for all or some of the diversity indices evaluated. Furthermore, this study shows that in the Chocó Region, Piper phylogenetic diversity increases with total number of species, but decreases with the proportion of endemics.