Solanum quitoense Lam., locally known as chila, is an underutilized fruit-bearing species native to the Andean-Amazonian region, traditionally cultivated in home gardens and smallholder farming systems. Despite its high nutritional, agroecological, and climate resilience, chila remains an orphan crop with limited genetic and genomic resources. To address this gap, the Universidad Nacional Toribio Rodríguez de Mendoza (UNTRM) launched a systematic program for the the collection and conservation of S. quitoense in the Peruvian Amazon region. The field expeditions, which covered all seven provinces of Amazonas, resulted in the establishment of a germplasm collection consisting of 31 distinct accessions, which are now conserved ex situ at UNTRM. This effort represents the first comprehensive initiative to document the genetic diversity of chila in this region. The accessions are currently undergoing molecular characterization using a combination of short- and long-read sequencing technologies. As part of this effort, we have begun assembling the complete chloroplast genome using long-read data, which will serve as a valuable genomic resource for phylogenetic and population studies. Future efforts will focus on nuclear genome sequencing and the development of molecular markers to support genetic diversity analysis, population structure inference, and the mapping of potential traits. These genomic tools will lay the foundation for pre-breeding and conservation strategies aimed at enhancing the crop’s resilience to biotic and abiotic stressors. This work is part of UNTRM’s broader program to promote the conservation, valorization, and sustainable use of native orphan crops from the Andean–Amazonian corridor. By unlocking the genetic potential of S. quitoense, we aim to contribute to the diversification of food systems, rural innovation, and climate adaptation in northern Peru.