Human activities have vital impacts on ecosystems. Deforestation is one of the most common human activities. Deforestation leads to reduced population sizes of the remnant plants, or leads to local extinction. When deforestation stops, population size of remnant plants may increase gradually and some extinct species may appear via seed dispersal. However, genetic composition of the restored populations may be changed due to bottleneck effect or founder effect. Theoretical studies have proven that deforestation has negative impacts on genetic variation, and that rare alleles are especially vulnerable to loss. However, there are few empirical studies concerning the genetic consequences of deforestation on plant species. East China has suffered from serious deforestation, and there is hardly any pristine forest remaining. Zonal vegetation in subtropical areas of East China is constituted largely by evergreen broadleaved forests (EBLFs). Castanopsis sclerophylla is one of the dominant species of EBLFs and is also one of the earliest evergreen plants to recover during the restoration process that follows after deforestation. Therefore, it is an ideal species to check the effects of deforestation on genetic variation. To study the effects of deforestation on genetic variation of Castanopsis sclerophylla, a total of 138 individuals were collected from 5 populations, among them two were from mature forests and three were from restored forests. We used microsatellites to detect the genetic composition. After screening the microsatellite primers available in congener species C. cuspidata var. sieboldii, we got five pairs of primer suitable for C. sclerophylla. Each individual was genotyped at the five microsatellite loci. The five loci revealed 29 alleles in the global population. Mean number of alleles per locus, effective number of alleles per locus and allelic richness of the global population were 5.80, 3.54 and 4.85 respectively. The observed heterozygosity (0.53) was significantly lower than the expected heterozygosity (0.72) (p<0.01). Within-population genetic diversity was high, and no significant difference was found between populations from mature forests and from restored forests. Little genetic differentiation (GST=0.028, FST=0.032) was observed among populations and the calculated gene flow was 8.68. Comparable genetic variation in populations from restored and mature forests indicated that deforestation in this region has not significantly reduced genetic diversity of C. sclerophylla, mainly due to its extensive sprouting. However, the software BOTTLENECK indicated a recent population bottleneck in 3 restored populations, a sign of distinct population decline in recent generations. A recent bottleneck was also observed in 1 mature population, mainly due to recent forest fragmentation.