Aim Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae , the Mountain Black‐eye, an endemic montane bird of Borneo with a sky‐isl...