Species dispersal patterns and population genetic structure can be influenced by large geographical features and habitat fragmentation. The Qinling Mountains are a major east-west mountain range and they are also the northernmost habitat of wild Cymbidium faberi in China. However, the impact of the Qinling Mountains and habitat fragmentation in the areas on genetic variation of C. faberi at population level is still poorly understood. Here, genetic analysis of C. faberi in the Qingling Mountains was conducted based on two chloroplast DNA sequences of 271 samples in 15 locations. Hierarchical analyses of molecular variance (AMOVA) and mantel test indicated that most of the genetic variance was within populations, genetic distance between populations was correlated with the geographical distance but not strong (mantel r = 0.505, P = 0.011). Spatial analysis of molecular variance (SAMOVA) indicated that the FCT reached the maximum value at K = 2 and then decreased, which supported a two-group genetic structure. Furthermore, the Extended Bayesian Skyline Plot revealed that the estimates of effective population size of C. faberi were under demographic equilibrium in the past but an apparent decline going from approximately 1 Ma towards the present. Moreover, we found that the genetic diversity of C. faberi in fragmented landscape was lower compared to continuous ones. Therefore, we concluded that the habitat fragmentation has restricted the gene flow of C. faberi by disrupting seed dispersal. Our findings may provide helpful references for understanding how humans shape the genetic structure and the importance of conserving wild orchids.