The levels and partitioning of genetic diversity and inbreeding depression were investigated in Tupistra pingbianensis, a narrow endemic of South-east Yunnan, China, characterized by a naturally fragmented distribution due to extreme specialization on a rare habitat type. Here genetic diversity and patterns of genetic variation within and among 11 populations were analyzed using AFLP markers with 97 individuals across its whole geographical range. High levels of genetic variation were revealed both at the species level (P₉₉ = 96.012%; H_t = 0.302) and at the population level (P₉₉ = 51.41%; H_s = 0.224). Strong genetic differentiation among populations was also detected (F_ST = 0.2961; ⍬^嘦= 0.281), which corresponded to results reported for typical animal-pollinated, mixed selfing and outcrossing plant species. This result was consistent with mating patterns detected by our pollination experiments. The indirect estimate of gene flow based on ⍬^嘦 was low (N_m = 0.64). Special habitat and its life history traits may play an important role in shaping the genetic diversity and the genetic structure of this species. A pollination experiment also fail to detect significant inbreeding depression upon F₁ fruit set, seed weight and germinate rate fitness-traits. Since naturally rare species T. pingbianensis is not seriously genetically impoverished and likely to have adapted to tolerating a high level of inbreeding early in its history, we propose this species need only periodic monitoring to ensure their continued persistence but not intervention to remain viable.