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Nonhuman primates have been observed to exchange friendly gestures soon after an agonistic episode, a behaviour labelled reconciliation. Frequency of reconciliation has been shown to vary both within and between primate groups. This study used both univariate and multivariate analyses to investigate intragroup variation in the frequency of reconciliation in captive Japanese macaques (Macaca fuscata). Frequency of reconciliation was lower during the mating season, and was also affected by the intensity of aggression and by the sex and age combination of the opponents. On the contrary, outcome of aggression and number of aggressors did not influence the frequency of reconciliation. Kin reconciled more than nonkin, and individuals with a good social relationship reconciled more than those with a bad or weak relationship. The effects of kinship and relationship quality appeared to be independent since among individuals with a good relationship, kin reconciled more than nonkin, while among nonkin, individuals with a good relationship reconciled more than those with a bad or weak relationship. Our results show that Japanese macaques are highly flexible in their conciliatory behaviour, and highlight a possible role of reconciliation in the negotiation and management of primate social relationships.