In sika deer Cervus nippon, rutting vocalizations play an important role in breeding behavior. This study investigated two types of rutting vocalizations, the moan and the howl, of the Formosan sika deer C. n. taiouanus, including the acoustic characteristics of the vocalizations, the diurnal and seasonal variations of vocal activity, and individual acoustic variation and identification. The results showed that the sound levels were approximately 81–88 dB(A) for the moan and 92–96 dB(A) for the howl, at a distance of 7 m from the sources. From October 2006 to January 2007, eight days of continuous observations were conducted to record the type and amount of vocalizations. Both moan and howl began to occur in the middle of October and reached peaks in the middle and end of November. Thereafter, few vocalizations were recorded until mid-January 2007. Moreover, we found that 74.5% of the first portion of moan, 65.3% of the second portion of moan, and 64.2% of howl could be identified on an individual basis by using discriminant analysis with 200 iterations of cross-validation test. These results revealed that the sounds differed among individuals, and also that they could be correctly identified. Our findings add to the scientific knowledge of sika deer behavior and provide the basis for a novel method of monitoring sika deer populations.