To evaluate the antimicrobial resistance of Vibrio parahaemolyticus isolated from shellfish and its habitat in Sichuan, Fujian and Guangxi.The susceptibility of 186 isolates of Vibrio parahaemolyticus to 8 antibiotics were determined by broth microdilution susceptibility test. The antibiotics of ampicillin, cefotaxime, ceftazidime, gentamicin, tetracycline, chloramphenicol, ciprofloxacin and trimethoprim/sulfamethoxazole were used.The antibiotic resistance rate were 69.35% in which ampicillin resistance was the most prevalent. The geometric mean of ampicillin MIC value of all isolates was greater than the interpretation value of resistance. Among the 186 tested isolates, the multiple antibiotic resistance and/or intermediate resistance was 4. All strains were 100% sensitive to cefotaxime, ceftazidime, chloramphenicol and ciprofloxacin. The ampicillin susceptibility spectrum of aquaculture farm was the highest among the three sectors as 73.68% and Sichuan was the highest among the three provinces as 70.94% although there were no significant differences. There were 44 samples out of which 2 and above strains were isolated, and the susceptibility spectrum polymorphism rate of strains isolated from the same sample was 77.27% (34/44).The ampicillin resistance rate is relatively high, and shellfish habitat may be the main source of antimicrobial resistance of Vibrio parahaemolyticus. There is an urgent need to strengthen the surveillance and management of Vibrio parahaemolyticus in the shellfish breeding process.