The fecal pellets and fecal pellet group characters of two ungulates, the Japanese serow and sika deer, were compared in Tokushima, Japan, where the species occur sympatrically. Species identification based on 82 fecal DNA samples revealed that 28 and 54 fecal pellet groups were from Japanese serow and sika deer, respectively. The mean values of three fecal pellet groups characters, the maximum diameter, the proportion of adherence of fecal pellets (maximum number of adhering pellets/total pellet number), and pellet number, were significantly different between the two species. These values reflect the differences in their defecation behaviors, and piled fecal pellet groups of Japanese serow can be clearly distinguished from those of sika deer. A stepwise discriminant analysis selected only one fecal pellet group character, the proportion of adherence of fecal pellets, and provided the highest correct classification rate (82.1% for Japanese serow and 88.9% for sika deer). The proportion of adherence of fecal pellets is an important parameter for discriminating between Japanese serow and sika deer on field surveys.