Multilevel societies (MLS), which have two or more levels of organization, are among the most complex primate social systems. MLS has only been seen in some primates, including humans. The aim of this study was to identify MLS in proboscis monkeys in Sabah, Malaysia, through direct observation (>32 months) and genetic analysis, based on feces collected from ~200 individuals, to estimate the degree of kinship. The results revealed that the social system of the proboscis monkey exhibited a form of MLS, with several core reproductive units and the bachelor group woven together into a higher-level band. Genetic analysis revealed that the females migrated randomly over short and long distances; however, the males tended to migrate relatively shorter distances than females. Combined with the results of direct observations, we concluded that proboscis monkeys form an MLS with a double or triple structure and patrilineal basis. The results of this study may have implications for the evolution of human societies, as to why patrilineal MLS, an important step in the evolutionary path of human societies, emerged in phylogenetically distant primates, such as the proboscis monkey.