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During exploration of chromosome polymorphisms in Japanese macaques, a heteromorphic polymorphism was found in a population in the Zigokudani monkey park. The population consisted of three troops (social units). Of 36 monkeys examined, five females showed heterozygotic 'marker' chromosome (chromosome 9). The polymorphism was a tandem duplication of the nucleolus organizer region (NOR) of the short arm of chromosome 9, which was found for the first time in the genus Macaca. FISH and fibre-FISH using human 18S rDNA and sequential silver nitrate staining revealed that the duplicated region included a part of the euchromatic satellite and the stalk and that the euchromatic block (intercalary satellite) divided the NOR into two parts (distal and proximal). Furthermore, it showed that the distal region possessed much more rDNA than the proximal region, and that the duplications might have been introduced via a mechanism of gene amplification (inverted duplications associated with over-replication and recombination events). As the tandem duplication was observed sporadically in four maternal pedigrees in two troops and the mothers of the variants all had normal chromosomes, the variation might have been introduced from another population's gene pool by a solitary male immigrant.