Paphiopedium micranthum is rare and endangered orchid known as slipper orchid. Its survival had been so seriously threaten that it lead to a drastic decline in number and range of wild population because of commercial need and habitation destruction In order to assess its influence on genetic structure of P. micranthum and provide fundamental information for its protection, 167 samples from seven populations under the different disturb circumstance in the over collection region were drawn to detect its genetic diversity and structure within and among populations by Sequence-related amplified polymorphism (SRAP) technology. Molecular marker revealed that it had a high level of genetic diversity at species level (PPB=81.25%; I=0.3709) despite small population sizes, a quiet low level at population (PPB=47.92%; I=0.2348), a moderate mean genetic distance among population (D = 0.1268). Analysis of molecular variance (AMOVA) indicated that the contribution (66.27%) of variability came within population level, which was consistence with the coefficient of genetic differentiation among populations (Gst=0.3568) result. P. micranthum maintained significantly higher population differentiation compared to other outcrossing orchid species. The current studies suggest that selective collection, habitats destroyed and fragmented lead to loss of genetic diversity within populations and aggravated gene differentiation In addition, a gene drift was very important reason responsible for a high gene differentiation adaptation evolution may be another reason for genetic differentiation. Genetic flow may be not the main factor for differentiation.