Although noncrop woody plants in crop field landscapes serve multiple functions, the modernization of agriculture has threatened their preservation. In this study, isolated woody plants used as farmland boundary markers were investigated in Ibaraki Prefecture in the eastern Kanto region. A total of 2001 individuals of 50 species were found around 177 equidistantly spaced points. The most frequently used species was Deutzia crenata (60.7%), and the main subordinate species were Pourthiaea villosa (8.8%), Euonymus japonicus (7.7%), Camellia sinensis (6.8%), Morus bombycis (4.6%), and Celtis sinensis (4.2%). According to multiple kernel density estimation, all six species were estimated to have at least one core area of high presence probability. Spatial segregation analysis of those species observed more than twice indicated that the marker usage showed significant spatial heterogeneity in the region. According to managers at 32 farms, marker plants are seldom used for other purposes. Trimming frequency of markers varied among the managers, even for the same species. Most of the managers did not know the introducer, introduction year, and marker plant source, except four managers who introduced or restored the markers using D. crenata (n = 2) and E. japonicus (n = 2). These findings suggest that the regional diversity of markers reflects historic species selection. Therefore, preservation of woody plant markers must be planned based on the local characteristics of biocultural resource usage.