The dataset of the Red Data Book vascular plants of Transbaikalia was created based on the latest editions of the Red Data Book of the Republic of Buryatia and the Red Data Book of the Zabaikalsky Krai (Russia). The dataset provides the most updated information regarding the distribution of 271 rare vascular plants (2920 distribution records). The distribution of the studied species was recorded during field surveys using GPS navigators, georeferenced from herbarium specimens, and digitised from printed distribution maps. Each entry in the dataset has various attributes, including belt zone, distribution, ecological, and life-form group features. Distribution patterns for various groups of rare and endangered species were analysed by means of QGIS 3.10 software. Our study has revealed a number of localities of vascular plants listed in the Red Data Book and clarified their distribution within the federal Protected Areas of Transbaikalia, among which Tunkinsky National Park has the highest diversity. Distribution of some rare and endangered species fall under federal protection, but some plants, including endemic species, require better protection. Analysis of various belt zones and distribution groups showed their distinct spread within the study region. Among the studied species, mesophytes and short rhizome perennial plants prevailed. It is also important to preserve vascular plants in the Red Data Book outside Protected Areas. Hence, information from our dataset can be useful for conservation monitoring programmes. Our study provides a basis for future conservation activities and can be applied in the establishment of new Protected Areas or Important Plant Areas in Transbaikalia.