An analysis of the microhabitat preference of the Alishan salamander (Hynobius arisanensis) was conducted in the Alishan area of Taiwan from 2003 to 2006. The study consisted of two parts: one to record microhabitat use of salamanders, and the other to quantify suitable microhabitat in the study site. The salamanders were found to use most of the microhabitat types available to them in the study site. However, they used rocks as shelters at a high frequency (77.7%). Although decayed logs were less available than rocks, the salamanders seemed to choose the logs as shelters. The decayed logs can keep moisture for a longer time and provide more prey than rocks, which probably causes the salamanders to choose less-available logs. The salamander preferred large rocks, but showed no preference for the size of logs. They also liked the cover objects with mosses growing on them. As for substrates, soil and plant debris were used most frequently. Salamanders were found negatively associated with live plant roots. Plant roots growing profusely under the cover objects are difficult for the salamanders to pass. The Alishan salamander preferred substrates with neutral substrate pH (6.2–7.0), high substrate moisture (70%–90%), and moderate substrate hardness (10–15). These results show that when information on microhabitat availability is taken into consideration, the real microhabitat preference of the salamanders does not agree with the descriptive results. We suggest that a quantitative approach should be taken for a habitat preference study, and that this information will be very useful for habitat restoration.