The aim of this study was modelling the spatial distribution of Lilium ledebourii (Baker) Boiss. based on ecological characteristics, in order to predict potential habitats for conservation of a rare plant. Knowledge of the spatial distributions of rare and threatened species and the underlying ecological factors plays an important role in regional conservation assessments and development planning. One potential means to complement the insufficient information concerning the distribution and site suitability of rare species is provided by species distribution modeling. Lilium ledebourii (Liliaceae), locally named “Susan-e-Chelcheragh” is an endemic and rare species growing on the highlands of Damash region in Gilan Province of Iran. The habitat of this species is under IUCN protection, Category III (Natural Monument) by the Iranian Department of Environment since 1976. The development of the distribution model required the integration of geographical information system (GIS), spatial, logical, analytical and statistical tools. First, we selected and studied the main resource variables such as elevation, geographical aspect, slope, soil and vegetation cover in L. ledebourii site including: Damash, Dorfak and Khanghah (Ardebil Province) by field investigations and literature. Topographical data in geographical information system (GIS) was analyzed and land-form characteristics were provided. Results were analyzed (statistical & logical) and effective factors on spatial distribution of L. ledebourii were introduced. Results were classified into two models including: conceptual model and quantitative-weighted model. Weighting in quantitative-weighted model performed based on Analytical Hierarchy Process compares the performance of two models indicating that the quantitative-weighted model was more accurate and effective than the conceptual model.