Long-term economic development of the ecosystems of the Baikal basin had a negative impact on the status of wildlife. Under these circumstances, it is necessary to develop monitoring systems and take up measures to protect the biological diversity of the area. This requires accurate information on the distribution of rare species and their present state. The authors present the results of mapping areas of rare species of vertebrates in the framework of the creating the Ecological Atlas of the Baikal basin. In a series of seven maps there is information on the distribution of rare species of animals grouped according to systematic criteria: fish (14 species), amphibians (4) and reptiles (6), birds (55) and mammals (28). Geographic maps of scale 1 : 5 000 000 served as the basis. It was to facilitate the orientation of the applied elements of hydrography, settlements, state and administrative boundaries. The obtained maps enable analyzing the spatial distribution of the species in the basin of the lake. It helps quickly obtain information about its conservation status and rarity category, which greatly facilitates the search and collection of information inaccessible to a wide range of users. The maps can also be used for monitoring and taking up security measures for rare species of vertebrates, developing recommendations for the conservation of their habitats under the conditions of intensive economic and recreational activities. Future prospects of Zoological mapping development associate with the development of geo-information technologies and creating databases for free access.