The activities of functioning and planning new transboundary protected natural territories inevitably require the availability and quality of cartographic rationale for the countries participating in the process. In many cases, the low involvement of near-border areas into economic activity provides a sufficient degree of ecosystem protection. The possibility of organizing transboundary specially protected natural areas appears in territories most significant in the view of preserving the natural diversity, adjacent to the borders of neighboring states, where arranging specially protected natural areas is extremely actual. The authors consider the task of applying the cartographic rationale at creating transboundary specially protected natural areas by the example of five territories operating at the beginning of 2019 in accordance with the concluded interstate agreements: “Altai”, “Dauria”, “Sources of Amur”, “Lake Khanka” and “Ubsunur Depression”. 10 planned transboundary areas with the following countries neighboring the Asian part of Russia are represented: Kazakhstan, China, Mongolia, North Korea, Japan, and the USA.