BACKGROUND: Understanding the emergence and spread of anti-malarial resistance, particularly to artemisinin and its partner drugs, is essential for eradicating malaria in worldwide. To identify genetic markers associated with susceptibility to common anti-malarial drugs, the in vitro sensitivities of anti-malarial drugs were evaluated, and a genome-wide association study of Plasmodium falciparum susceptibility in vitro to multiple anti-malarial drugs was conducted. METHODS: Genomic DNA from 34 samples of P. falciparum collected between 2007 and 2010 in the Nabang-Lazan Valley along the China-Myanmar border was extracted and subjected to whole-genome sequencing. The standard SYBR Green I-based fluorescence assay and RSA assay were used to evaluated the in vitro sensitivities of anti-malarial drugs. Plink v1.90 was used to investigate the associations of genome-wide SNP with in vitro sensitivities to anti-malarial drugs. RESULTS: The proportion of isolates showed reduced-susceptible to CQ,SP,QN,PPQ and PND were 88.24%,92.59%,8.82%,8.82%,5.88%, respectively. 93.54% of isolates showed high level of the IC CONCLUSIONS: Multiple genetic markers correlating with anti-malarial drug susceptibility were identified in the study, which provide a reference for further investigations into the association between oxidative stress-mediated activity and anti-malarial drugs susceptibility.