Harlequin is a coat pattern of the Great Dane characterized by ragged patches of full color on a white background. Harlequin patterning is a bigenic trait, resulting from the interaction of the merle allele of SILV, and a dominant modifier locus, H. Breeding data suggest that H is embryonic recessive lethal and that all harlequins are Hh. To identify linkage with the harlequin phenotype, 46 Great Danes from 5 pedigrees were genotyped for 280 microsatellite markers in a whole genome screen. One marker on the telomeric end of chromosome 9 was suggestive of linkage. Fine mapping of this region using additional microsatellite markers and 10 Great Danes from a sixth pedigree resulted in significant LOD scores for 2 markers. Reported herein is linkage mapping of the H locus to a 3.27 Mb region of chromosome 9 containing approximately 20 genes.