Apple (Malus ×  domestica) is a main fruit crop of cold temperate regions and traded globally. Despite being a comparatively well-documented plant cultigen, available germplasm in many remote regions is still unexplored and threatened. Increasing market demands for modern varieties and farmers’ preference for high yields may lead to the gradual loss of local and indigenous varieties. Gilgit-BaltistanGilgit-Baltistan in Northern Pakistan—a mountainous and remote apple-growing region—was selected to study local cultigens diversity by assessing varietal richnessVarietal richness and diversity, arboriculture activities as well as phenotypic and genotypic characters of available germplasm. In total, 106 individual apple trees were sampled, and 35 tree owners were interviewed from seven villages of the two valleys Ishkoman and Baltistan. Dendrometric parameters, fruit traits (qualitative and quantitative), and varietal diversityVarietal diversity in each village were measured. Genetic variation was estimated using 11 SSR markersSSR marker and synonymsSynonyms and homonymsHomonyms were identified based on cluster analysis. Sixty-one multi-locus genotypes (MLG; mean genotype diversity: 58%) and 18 putative clones (comprising 2–9 ramets) were identified. Varietal diversityVarietal diversity was highest in Baltistan where even a wild apple relative (Malus baccata) was discovered. Mean genetic diversityGenetic diversity was moderate (He = 0.677), while negative inbreeding coefficients indicated excess of heterozygotes in three genetic clusters. A moderate correlation (r = 0.627, p = 0.001) between phenotypic andGenetic dendrogram genetic dendrogramsDendrogram suggested genetically linked fruit traits, which merits further exploration. Considering the high genetic and phenotypic variability, Gilgit-BaltistanGilgit-Baltistan appears a promising source of apple germplasm for future breeding programs. The promotion of local varieties may allow farmers to diversify their produce and derived sources of income as well as to maintain a historically important biological heritage of Gilgit-Baltistan. To this end comprehensive conservation strategies combined with participatory research will be needed.