Hybridization and introgression are thought to be important for speciation and adaptation in many plants. However, little is known about the hybridization and introgression among Cypripedium species. To investigate the evidence for hybridization and the pattern of introgression between Cypripedium yunnanense and C. tibeticum in Shangrila County, Yunnan Province, China, morphological characters and amplified fragment length polymorphism (AFLP) data for both the species and their putative hybrids were studied. Hand pollination was also performed to verify the crossability of the putative parents. Principal coordinate analysis based on morphological characters and the AFLP data suggested that the putative hybrids were true hybrids of these two Cypripedium species. Analysis with the NewHybrids software indicated that the putative hybrids were F1 generation individuals and backcrosses to C. yunnanese, but no F2 generation was found. Analysis with the Structure software demonstrated asymmetric introgression from C. tibeticum to C. yunnanense. We conclude that natural hybridization and introgression can occur between these two species and that in situ conservation of the parental species is required before fully assessing the evolutionary potential of hybrids.