Euptelea pleiospermum is an ‘‘old rare’’ tree species distributed along the high-elevation streamsides in Burma, China, and India. Deforestation and construction of roads for timber transport have highly fragmented the natural habitats of this species in the Shennongjia Forestry District. In this study, we used this fragmentation to test the hypothesis that ‘‘old rare’’ tree species are insusceptible to the genetic consequences of habitat fragmentation. Using eight microsatellite loci, we estimated allelic richness (AR), observed heterozygosity (HO), expected heterozygosity(HE), Wright’s inbreeding coefficient (FIS), and genetic differentiation (FST and DEST) between preand post-fragmentation cohorts. We found no significant differences in either genetic diversity or genetic differentiation between the two cohorts. The limited genetic effects of fragmentation may result from too few fragmented generations, because the time between the start of fragmentation (year 1970) and our study (year 2008) was less than one generation of this tree species. It should be mentioned that clonal reproduction by sprouting, a common phenomenon in many ‘‘old rare’’ tree species, can help E. pleiospermum buffer the genetic impacts of fragmentation by delaying the time between generations. Therefore, we conclude that this ‘‘old rare’’ tree species show limited genetic impacts from recent habitat fragmentation. However, the elimination of rare alleles and increase of inbreeding coefficient in the post-fragmentation cohort are early warnings of deleterious genetic consequences of fragmentation. Our results provide valuable information to formulate conservation and restoration guidelines for E. pleiospermum.