Presented are the results of investigations made in 2013–2014 with the purpose of developing the system of biodiversity monitoring on the specially protected natural territories within the Lake Baikal drainage basin. The investigations used model areas, i. e. specially protected natural territories (Baikalsk State Nature Biosphere Reserve (Zapovednik), Zabaikal’skii State National Park, and Kabansk State Nature Reserve (Zakaznik)). The existing methodological level of biodiversity monitoring is outlined, and an array of scientific and scientific-organizational problems in carrying out observations is revealed. The investigations resulted in the development of the Program of biodiversity monitoring in the state nature reserves and national parks of the Baikal natural territory as well as the methodological recommendations for its implementation. It is shown that the development of a unified program of long-term biodiversity monitoring must be based on the novel methodological approaches and techniques and that there is a need for an obligatory unification of all the main techniques used in collecting data within the «Nature Records» program.Keywords: unified program, system of observations, abiotic parameters, objects of monitoring, biodiversity data bank, Baikal natural territory.