In the present study, the drug-resistance genes encoding β-lactamases, aminoglycoside modifying enzymes, DNA topoisomerases and integron as well as their molecular epidemiology were investigated by means of analyzing the drug-resistance and molecular epidemiology of Acinebacter baumannii isolated from the clinical samples in two hospitals in Changzhou and Huzhou city of Jiangsu and Zhejiang province from July 2000 to March 2005. The minimal inhibitory concentrations (MICs) of these 307 isolates were detected by automatic microbiological system, and 35 strains against 5-fluoroquinolones were performed by agar dilution assay. Meanwhile, the resistant genes in 80 isolates were amplified by PCR with identification by DNA sequencer. It was found that most of the 307 isolates of A. baumannii were resistant to multiple antibiotics tested, in which the resistance rates of the isolates against piperacillin, piperacillin/tazobactam, amoxacillin/clavulanic acid, cefotaxime, ceftazidime,cefepime, gentamicin, amikacin, ciprofloxacin, chloramphenicol and sulfamethoxazole/trimethoprim were all above 35%, but those of imipenem and meropenem were quite low, ranged only 2.6% and 3.3 %. In addition, it was also demonstrated that the positive rates of TEM and SHV β-lactamase genes accounted for 93.8% and 22.5% respectively, and those of the aminoglycoside-modifying enzyme genes including aacC1, aacC2, aacC3, aacC4, aacC4A, aphA6, ant(2")-Ⅰ and ant(3")-Ⅰ were 58.8%, 8.8%, 7.5%, 28.8%, 45.0%, 2.5%, 28.8% and 65.0% respectively. The mutations in the quinolone-resistant determining region (QRDR) of gyrA and parC genes indicated that substitution in Ser-83 residue of GyrA protein was most frequently occurred among strains with MIC for ciprofloxacin of more than 4 μg/ml, whereas a double mutation at Ser-83 residue of gyrA and Ser-80 of parC was found in strains with MIC of ciprofloxacin of more than 8 μg/ml. As to the positive rates of class 1 integron (Int Ⅰ -1) and qacE△1-sul-1, it was found to be 60.0% and 77.5% respectively,and the rates of resistant genes of strains isolated in these two hospitals varied considerably. The results obtained in the present study indicate the presence of the multiple resistant genes in strains of A. baumannii, and great measures should be taken to control the spread of the resistant strains carrying the resistant genes.