The nombre fondamental (NF), which is the total number of euchromatic chromosome arms in the female, is the same in the Finnish as in the Japanese raccoon dog, 66. However, the karyotype of the Finnish raccoon dog consists of 5 metacentric and 21 acrocentric autosome pairs whereas that of the Japanese raccoon dog has 13 metacentric and 5 acrocentric autosome pairs. In both, the X chromosomes are medium-sized and metacentric and the Y chromosomes small and metacentric with satellites. The number of B chromosomes varies from 2 to 4 in the Finnish and from 2 to 5 in the Japanese raccoon dog, the number varying within and between individuals.
A comparative chromosome study using GTG-banding showed Robertsonian translocation as the main mechanism of chromosome evolution since many chromosome arms had identical banding patterns. The B chromosomes were acrocentric, CBG-positive, and late-replicating; they were larger in the Finnish than in the Japanese raccoon dog. In both, three autosome pairs had NORs in addition to the NOR in the Y chromosome. Whether hybrids can be produced between these chromosomally-different raccoon dogs is not yet known.