Forest ecosystems are rich in biodiversity and provide valuable ecosystem services, but are declining worldwide. Malus niedzwetzkyana, an Endangered wild relative of domesticated apples, is an important component of the walnut–fruit forests of Central Asia. Its iconic pink blossom and genetic properties give it special cultural and scientific significance, but livestock grazing and firewood collection threaten its survival. The conservation of the species and its native forest ecosystem is critical and urgent. This study provides information on the ecology and population of M. niedzwetzkyana and the threats affecting its habitat, improving our understanding of its distribution and proposing measures to reduce threats. We collected ecological data and assessed population structure and threats at four forest sites in southern Kyrgyzstan. We mapped 149 individuals, creating the largest known dataset for this species. We developed species distribution models for M. niedzwetzkyana to identify climatically suitable regions and potential areas for restoration. Sary-Chelek Biosphere Reserve contained the largest expanse of pristine forest and the most stable M. niedzwetzkyana population, followed by Kara-Alma Forestry Unit. Forests in the Gava Forestry Unit and Dashman Reserve were most extensively damaged by humans and livestock. The wild apple's favoured habitat was south-west facing slopes with a gradient < 30° and a relatively open canopy. Overall, the study population was vulnerable to extinction with limited regeneration potential. We recommend short-term population enhancement through planting projects and increased protection of individuals in pristine sites. Community-based conservation initiatives should be prioritized in extensively damaged sites, and larger-scale reforestation of these forests needs to be considered.