The genus Pristimantis contains many species and species groups that are difficult to differentiate. These frogs show high intraspecific morphological variability and low morphological divergence between species, which contributes to misclassification of taxa and systematic uncertainties. Morphometric assessments coupled with the use of molecular markers are opening new avenues to resolve the taxonomy of this group, allowing for identification of informative characters. Morphometric and genetic analyses were applied to differentiate three species of Pristimantis (P. calcaratus, P. kelephas, and P. jubatus) previously confused in their identification and description. We evaluated 51 qualitative and quantitative morphological characters with sequences of two mitochondrial (mt) genes (16S and cytochrome oxidase subunit I [COI]). We used discriminant analysis to show that these species could be differentiated by two qualitative morphological characters (posterior surfaces of thighs and longitudinal stripes on the dorsum), whereas one quantitative variable (distance from tympanum to eye) differentiates only adults of the three species. Our genetic data showed highest divergence in comparisons of P. jubatus (>13%) with the other two species, whereas comparisons between P. kelephas and P. calcaratus were 2.6% and 8.3% for 16S and COI, respectively. These differentiations suggest that they are well-delimited species on the basis of morphological and mt deoxyribonucleic acid data. Nevertheless, the genetic differentiation between P. calcaratus and P. kelephas implied a recent divergence and showed the importance of using both morphometric and genetic analysis in species recognition.