Isolated trees in farmlands serve various ecological functions, but their distribution patterns and planting history are often unknown. Here, we examined the spatial distribution, uses, and folk nomenclature of farmland demarcation trees planted in the Niyodo River area in Japan. Hierarchical clustering using the data from 33 locations distinguished four tree composition groups characterized by the combination of Euonymus japonicus, Ligustrum obtusifolium, Deutzia crenata, and Celtis sinensis. Near the upper to middle reaches of the river, the group characterized by E. japonicus dominated. Near the middle to lower reaches, the group characterized by L. obtusifolium occurred relatively frequently. The other two groups were found sporadically near the upper to lower reaches. The locally unique plant name nezu, used for L. obtusifolium, seems to have originated from a word meaning “the tree does not sleep and keeps the watch” in Japanese. In the study area, D. crenata was one of the plant species utilized for the sticks (magozue) used in traditional funeral ceremonies, which might help to explain why local people maintain D. crenata around homesteads as a demarcation tree. These findings highlight both the commonalities and uniqueness of demarcation tree culture in different regions of Japan and contribute to deepening our understanding of agricultural heritage.