<p>Growing concerns over food security, agrobiodiversity loss, and climate change drive renewed interest in underutilized crops with high agronomic, nutritional, and adaptive potential. <i>Capsicum pubescens</i> Ruiz &amp; Pav. is one of the five domesticated chile peppers and a distinctive crop of Andean agriculture. Adapted to cool mountain environments and characterized by its conspicuous pubescence, purple flowers, and dark seeds, it has long played important culinary, cultural, and economic roles across the Central Andes. Despite its uniqueness, <i>C. pubescens</i> remains understudied compared to other chiles, with no comprehensive synthesis available to date. This review addresses this gap by synthesizing current knowledge on the evolutionary history, domestication, diversification, genetic resources, and biocultural significance of the species, integrating recent genomic advances with taxonomic, eco-geographical, agronomic, and historical evidence. Genomic research reveals substantial genetic variation within <i>C. pubescens</i>, with the highest diversity in Bolivia and distinct northern and southern lineages shaped by human-mediated dispersal across the Americas. Available evidence supports a Central Andean origin and suggests the inter-Andean valleys of the Bolivian Yungas as the primary center of diversity and a leading candidate region for domestication. However, these scientific advances contrast sharply with major gaps in germplasm conservation, particularly the underrepresentation of Bolivian landraces and wild relatives in public ex situ collections. Leveraging these emerging genomic resources will therefore be essential to bridge these conservation gaps and accelerate breeding programs. Ultimately, unlocking the genetic and nutraceutical potential of <i>C. pubescens</i> represents not only a strategic pathway for climate-resilient agriculture but also a priority to safeguard an overlooked biocultural and evolutionary legacy.</p>