This pilot study reveals the polymorphisms of CYP2D6 gene coding region and its association with the recurrence of vivax malaria in the population of Yunnan Province, suggesting that the radical cure of vivax malaria by using primaquine could be hampered due to the impaired CYP2D6 enzyme activity in the population of Yunnan Province. This evidence concerns the gene CYP2D6 and Plasmodium vivax malaria.