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Wild grapevine, Vitis vinifera subsp. sylvestris is considered as a rare species in Europe and Iran and possesses restricted distribution due to threatening factors. Natural populations of wild grapevine in the north of Iran were evaluated in three wild areas of coastal and plains areas of Miankaleh, submontane areas of Amol and the forest patches of Kojour and a cultivated sample of crop grapevine, V. v. subsp. vinifera in Babolsar. A total of 41 anatomical traits and important ecological factors such as soil and climatic variables were investigated and included in further analyses. Anatomical characteristics of leaf blade and petiole had the most important impact on the separation of wild and the cultivated taxon. All the soil and climatic factors, particularly altitude and annual rainfall were significant between studied stations. Mean temperature of the warmest month along with soil clay and calcareous percentage had the highest effect and relationship with the anatomical traits. Based on the current result, anatomical characters can be used for separation between wild and cultivated populations. They are also effective in separation of different populations of wild grapevine. Quantitative anatomical changes in the studied populations are reflection of the different soil and climatic conditions of their habitat.