In order to assess importance of isolated forests as the wintering habitat of the sable (Martes zibellina) in eastern Hokkaido, Japan, we performed DNA analyses on 59 samples noninvasively collected in field (54 fecal, 3 urine and 2 hair samples). Consequently, 46 (41 fecal, 3 urine and 2 hair samples) of the 59 samples were recognized to have dropped from the sable. In addition, we successfully identified the individuality on 36 (35 fecal and 1 urine samples) of the 46 samples, and they consisted of at least 23 individuals. Our new method using sex chromosomal DNA markers showed that the 23 individuals comprised 12 males, 9 females and 2 with unknown sex. In 2010 and 2011, the minimum number of individuals in the study area was 21 (11 males, 8 females and 2 with unknown sex) and 5(1 male and 4 females), respectively. In addition, we found the sexual difference in fidelity to their home range. Thus, our noninvasive DNA technique provided promising information on estimating and monitoring ecological features about the regional sable population.