In the northern hills of Uruguay, our study employs intra-specific phylogenetic diversity to prioritize conservation efforts for four co-distributed frogs and lizards. Analyzing the ‘Quebradas del Norte’ region, we identify ‘Tres Cruces’ as a key area for protection, complementing existing phylodiversity. Patterns suggest limited species dispersal and distinctiveness of ‘Tacuarembó Grande/Cuñapirú.’ Our findings align with prior assessments, emphasizing the importance of considering genetic data for effective conservation prioritization in this region. We advocate for the use of the ‘areaPD’ R package for comprehensive phylogeographic analysis.