This article explores how the sense of territoriality and various background conditions of Japanese rural communities affect the emergence of folk boundaries, which are viewed here as the contours of residents’ cognitive territory represented by religion-based symbolic markers. Specifically, I look at how the particular social-geographical conditions of different communities create diverse conceptions of such boundaries, including the presence or absence of the boundaries, within the same region. Here, I focus on three Japanese villages encompassing seven local religious communities of Shinto-Buddhists, Catholics, and former Hidden Christians on Hirado Island in Kyushu. These villages are viewed respectively as examples of contrastive coexistence, degeneration, and expansion in territoriality. Among the seven religious communities, only those believing in Shinto-Buddhism, as well as Hidden Christianity, have maintained their folk boundaries. These communities satisfy the conditions of an agglomerated settlement form, a size generally larger than ten households, a location isolated from other communities within the village, and strong social integration. In contrast, Catholics have not constructed such boundaries based on their historical process of settlement. However, they have influenced the forms of Shinto-Buddhists’ territoriality, although not those of Hidden Christians. Additionally, their settlement form and relative location among the other religious communities have affected the shape of the Shinto-Buddhists’ cognitive territories. Changes in these intertwined background conditions can transform the states of territoriality, which should be viewed as correlated rather than independent and as dynamic rather than static.