Along the Czech-German border there are four national parks, two Czech and two German, arranged in cross-border ‘pairs’. This article focuses on the southern ‘pair’ formed by the parks of Šumava and Bayerischer Wald (Bavarian Forest). The aim is to evaluate and compare tourism organization in their areas, taking into account selected aspects of management: the network of hiking trails with its related infrastructure, transport accessibility, a typology of tourist centers, as well as directions and destinations of tourist movements. Based on the results, it can be concluded that the availability of geographical space for tourists is much greater in the German than in the Czech national park, and the tourism infrastructure is clearly more extensive there, including the network of tourist trails. This is mainly due to the longer and fairly uninterrupted development of tourism in this area. Šumava National Park can be identified as a model in terms of how to adjust the directions of tourist movements and the layout of the tourist trail network to the needs of natural environment. On the basis of observations in both national parks, it is possible to indicate various solutions that, after appropriate adaptation, may bring benefits to other protected areas.