Because evolutionary processes such as genetic drift and natural selection play a crucial role in determining the response that species will have to human-induced disturbances, there is increasing interest in the evolutionary aspects of conservation biology. Harvesting select individuals in natural plant populations can bring about unforeseen impacts that may negatively affect fitness. We analyzed how human harvesting affects two congeners known as snow lotus. Over a period of 100 years, there was a negative trend in plant height (r2= 0.4361, P < 0.001) for the intensely collected and rare species, Saussurea laniceps, but not in the less intensely collected species, Saussurea medusa. Additionally, S. laniceps were significantly smaller in areas of high harvest than in areas with low harvest (Z = 4.91, P < 0.0001), but this was not so for S. medusa. Humans can unconsciously drive evolution and must be considered when managing threatened species.