Abstract: Combining line-transect method and sampling method, the geographic coordinates of footprint links for Williamson’s Mouse-deer (Tragulus williamsoni) were collected in Mengman and Longmen regions of Mengla area, southern Yunnan, from June to December 2007. A distribution pattern map of the mouse-deer was produced by GIS software. Eleven ecological factors were measured in collected and available samples. The results indicated that the mouse-deer preferred valleys along banks of rivers or streams in low altitude, and were mainly distributed in Sanchahe of Mengman region and Darongshu of Longmen region. Comparing nominal factors between collected and available samples, the results showed that the mouse-deer tended to inhabit middle and lower slopes and favored the plant species of Ficus hirtal, Baccaurea samiflora, Alpinia kwangsiensis and Phrynium capitatum. These plants occur along banks of rivers or streams, one of the important reasons affecting distribution of the mouse-deer populations. Comparing quantitative factors between collected and available samples, the results showed that four factors including tall tree coverage, shrub coverage and herb coverage, and distance to water, were significantly different. These four factors were key in discriminating collected and available samples and main factors affecting the habitat use of the mouse-deer. The dense shrub with taller trees could form good shady condition for the mouse-deer, and greatly strengthen their security. Due to their preference for areas near water, there were more flourishing tall trees and dense shrubs at valleys in low altitude, which was one of important reasons affecting the distribution of the mouse-deer populations massing in valleys in low altitude.