Local crops are generally valued for their adaptation to specific ecological and agricultural conditions. However, this study examines contrasting socio-ecological dynamics in the mountainous Itsuki-Gokanosho area of Japan. Here, the taro variety Takenoko-imo (Colocasia esculenta) persists despite significant ecological and agronomic constraints. An interdisciplinary approach was used that combined ecological surveys with socio-cultural analysis. We found that Takenoko-imo is well-established as a local crop. It continues through intergenerational transmission and local circulation. Yet it mismatches local conditions, such as high frost vulnerability and a poor fit with historical shifting cultivation systems. These findings indicated that the persistence of local crops could not be explained solely by ecological or agronomic adaptation. Instead, it reflects the interaction among environmental constraints, social networks, market relations, and daily practices. Thus it was suggested to reconsider the role of human-mediated processes in sustaining agrobiodiversity in marginal rural areas.