Nationwide depopulation in modern Japan has led to contrasting changes over the last half‐century: shrinking human communities and recovering populations of Japanese macaques (Macaca fuscata). These changes have triggered macaque damage to public livelihoods, often resulting in decision‐making directed toward strictly regulating macaque populations. To optimize conservation interventions required today, we aimed to identify macaque habitats with conservation priorities to enhance population connectivity. To quantify the current population connectivity, we conducted a least‐cost path analysis by assigning an inverse of habitat suitability as resistance. For this, we collected geo‐information on home ranges of 2288 troops, accounting for >70% of the total number of troops in Japan. Moreover, we composed a minimum spanning tree using least‐cost paths to provide optimal population connectivity. Consequently, the modeled resistance showed that, although human‐induced barriers (i.e., flat areas where people frequently reside) and geographical barriers (i.e., alpine regions >1500 m above sea level) had the highest dispersal cost, macaques presented a high plasticity in the occupation of different forest types. The minimum spanning tree, composed of 77 modeled corridors, detected the vulnerability of population connectivity in western Japan and assigned conservation priorities to these isolated populations to preserve the stepping‐stone paths of macaque movement.