The aim of the present study was to determine whether, and to what extent, the isolation of Daphne malyana populations in the canyons, as refugial habitats, may have caused the morphoanatomical variability of this ancient endemic species. The specimens of D. malyana were collected in May 2008, during the flowering season, in four different sites in W. Serbia and N. Montenegro. The collected plant material was either placed in the herbarium or fixed in 50% ethanol. Voucher specimens of the plants were deposited in the Herbarium of the Institute of Botany and Botanical Garden Jevremovac, Faculty of Biology in Belgrade, Serbia. Comparative of morphoanatomical studies have shown the presence of general adaptive characteristics of a specific, conservative xeromorphic type, slightly differing in each population. Principal component analysis (PCA) and canonical discriminant analysis (CDA) of 20 morphoanatomical characteristics of the leaves and stems have shown a clear distinction between the populations from the river Piva canyon (Montenegro) and those from the Sokoline ravine (Serbia), on the one side, and those of Vranjak gorge (Serbia) and of the river Tara canyon (Montenegro) on the other side. It may be assumed that the mild morphological variability of the isolated populations of the Balkan endemic species Daphne malyana in the canyons and gorges seem to have affected by the microclimate conditions in their habitats.