Summarized the results of previous studies, the body size of Niviventer coxingi seemed to be correlated with altitude. For more exact evidence, geographic variations of body lengths and appendage sizes among areas were examined. Moreover, Freckleton et al. (2003) indicated that phylogenetic relationships may affect the results of one¡¦s study while variation of body size is discussed. Therefore, the phylogeographic variation among different areas was also examined in this study. The body lengths of N. coxingi in higher altitude (Fong-gang, 1700 m) were shorter than in lower altitude (Shan-ping 700 m). Body lengths of N. coxingi in Shan-ping were longer than other areas but Wu-shih-kang; and N. coxingi in Fong-gang were longer than those in Wu-tou Mountain; but no significant differences were found among other areas. No significant differences were found in appendage sizes but hind-foot length. Significant differences of the hind-foot length were only found between Shan-ping which had the longest hind-foot lengths in average and those in Wu-tou Mountain which had the shortest. No correlations were found between altitudes and the body length or appendage sizes of N. coxingi. The phylogenetic relationships based on D-loop region of N. coxingi were reconstructed by neighbor-joining, maximum parsimony and maximum-likelihood methods. An N. culturatus was used to be an outgroup. All three trees represented similar patterns. Although some individuals from neighborhood grouped together, some individuals from the same area represented distantly. Moreover, many branches represented in the root of the consensus trees because of the low bootstrap value. The results revealed the geographic variations did not correlated with their phylogenetic relationships and the heat conservation/ dissipation mechanism, which was the traditional explanation of Bergmann¡¦s rule, was not appropriate for N. coxingi, either.