Cytogenetic mapping of the arctic fox and the Chinese raccoon dog were performed using a set of canine probes derived from the Bacterial Artificial Chromosome (BAC) library. Altogether, 10 BAC clones containing sequences of selected genes (PAX3, HBB, ATP2A2, TECTA, PIT1, ABCA4, ESR2, TPH1, HTR2A, MAOA) and microsatellites were mapped by fluorescence in situ hybridization (FISH) experiments to chromosomes of the canids studied. At present, the cytogenetic map on the arctic fox and Chinese raccoon dog consists of 45 loci each. Chromosomal localization of the BAC clones was in agreement with data obtained by earlier independent comparative chromosome painting. However, two events of telomere-to-centromere inversions were tentatively identified while compared with assignments in the dog karyotype.