Eye colour in Japanese macaques shows apparent differences between individuals, continuously ranging from orange (bright), through shades of yellow and hazel-blue to dark blue (dark). We arbitrarily classified them into either ‘yellow’ eyes or ‘blue’ eyes based on the yellow area occupying in the iris’ peripupillary ring. Most Japanese macaques have yellow eyes after infant phase, whilst 19, 17, 12, and 15% of monkeys (>6 months, sexes combined) have blue-eye in studied two groups of Shodoshima and two groups of Takasakiyama, respectively. Frequency of eye colour did not differ between males and females, but significantly differed in each age class. Blue eyes significantly more frequently occurred in newborns, infants and aged monkeys than in juveniles and prime adults. Data from mother–infant pairs indicated eye colour could be inherited from their parents. A case of asymmetric eye colour in Japanese macaques was found from a sample of 1962 individuals. Eye colour variation of Japanese macaques was discussed in relation to those of humans and rhesus macaques. A possible evolutionary model of eye colour in Japanese macaques was discussed.