The Colombian Tropical Andes constitute an important area in terms of diversity and endemism of amphibian species. However, some studies have documented gaps in taxonomic information in these regions due to a lack of exploration, especially in the highest areas. The Parque Nacional Natural Farallones de Cali (PNN Farallones de Cali) is a protected area located in southwestern Colombia that brings together the Tropical Andes and Tumbes-Chocó-Magdalena biodiversity hotspots. This protected area holds a historical record of 112 named amphibian species, of which 36 are threatened according to the International Union for Conservation of Nature (IUCN) Red List, and 44 are endemic to Colombia. However, the highest peaks of this national park have remained unexplored due to the political instability of the country, the presence of illegal productive activities, and operational and logistical difficulties of access. Fortunately, owing to the combination of human and institutional efforts, possibilities for exploration and the development of scientific activities have become available in the last decade. During recent explorations of the high Andean forest and páramo ecosystems of the PNN Farallones de Cali, we discovered two new threatened species within the Pristimantis leptolophus species group based on molecular, bioacoustic, and morphological evidence. The first species is distinguished by its polymorphic coloring patterns, the small size of the males, the presence of a small papilla at the tip of the snout, and its advertisement call, which is composed of a stereotyped group of 3–10 tonal notes that are widely separated by intervals of silence. The second new species is distinguished by the presence of a small papilla at the tip of the snout and by lacking dorsolateral folds. These findings emphasize the importance of preserving the Andean and páramo ecosystems, which are home to several amphibian species and numerous others that remain undiscovered, highlighting the need to continue to explore uncharted areas in the Colombian Andes for a better understanding of Colombian amphibian diversity.