The present study explored the habitat suitability for an endangered species, Hedysarum criniferum, in Iran using fuzzy logic. We measured 24 environmental variables including soil, climate, and physiographic variables of eight natural habitats of H. criniferum as the predictive variables and the percent cover of the species as the response variable. The most important environmental factors influencing species distribution and the species response curves were determined by principal component analysis (PCA) and the generalized linear model, respectively. The tolerance range and the optimal growth point of the studied species with respect to the environmental factors were specified, the ranges were divided into 11 classes by fuzzy value, and the fuzzy functions of the environmental factors were calculated. The species habitats were classified by the developed fuzzy model. Three regions with no H. criniferum occurrence were selected to determine their fuzzy suitability. The success in germination and shoot growth length of H. criniferum were used as the metrics of the habitat suitability in these regions. Based on the PCA, H. criniferum occurrence was most strongly affected by soil Mg, K, and Ca content, soil pH, wind speed, annual minimum temperature, slope, and altitude. The results revealed that the seedling length and germination percentage in the site with the fuzzy suitability of 0.6 differed from those in the two other sites with the fuzzy suitability of 0.5 and 0.3 significantly. The method used in this study can be employed in predicting optimal habitats for other endangered species in different ecosystems.