We investigated genecology and ecophysiological mechanisms of the polymorphism of leaf trichome density of Leptospermum recurvum Hook. f. (Myrtaceae) in the deglaciated summit zone above 3,000 m asl of Mt. Kinabalu, Borneo. Various phenotypes with variable foliar trichome densities occurred sympatrically in the same population, and the composition of coexisting phenotypes varied substantially among populations. We conducted a common garden experiment by sowing seeds from multiple maternal trees of different leaf trichome densities. We found a significant relation between pubescence of maternal trees and offspring, which indicated that leaf trichome density had a genetic basis. Microsatellite analysis revealed that there was no barrier to gene flows among phenotypes or among populations, and very low neutral genetic differentiation among populations with high gene flows for both directions of phenotypes. The soils in the sites dominated by pubescent trees were significantly more desiccated than in the sites dominated by glabrous trees during a short drought. Glabrous trees had a significantly greater mortality rate than pubescent trees after an intensive El Nino drought (13.7 vs. 3.9%) in the same sites where both phenotypes occurred sympatrically. Pubescent individuals demonstrated a significantly greater photosynthetic water-use efficiency than glabrous individuals. El Nino droughts could cause large difference in soil moisture among sites and that a greater desiccation stress removed glabrous phenotypes as one end of divergent natural selection to form pubescent populations. These results implied that the process shaping the phenotypic polymorphisms involved strong gene flows combined with ongoing divergent selection.