Background: Acinetobacter baumannii is a significant nosocomial pathogen around the world, especially in the intensive care unit that most A. baumannii infections are caused by the outbreak strains. Objectives: This study has been performed in Acinetobacter baumannii isolates, aimed to detect integron classes I, II, III and molecular typing of A. baumannii genes. Methods: In this Cross-sectional study, Acinetobacter baumannii isolated from 150 patients in Isfahan hospitals then antibiotic resistance pattern was determined by disk diffusion method (Kirby Bauer). The presence of genes coding in antibiotic resistance and integrons class I, II, III were analyzed by using of M-PCR method. The data were analyzed by Chi-square, Fischer's test and SPSS statistical software version 16. Results: Antibiotic resistance pattern for Acinetobacter baumannii show that the high resistance was for ciprofloxacin with frequency of 98.3%, ceftazidime with 89.4%, and tetracycline with frequency of 87.3%. The most sensitive antibiotics were chloramphenicol, and nitrofurantoin with frequency of 3.5% and 3.2% resistance. The detection of dfrA1 (63.7%), sul1 (68.6%), aac (3)-IV (54.4%), tet (B) (22.4%), tet (A) (78.3%), aadA1 (15.4%), CITM (17. %), vim (12.2%), Qnr (17.1%), blaSHV (19.8%), sim (7.8%), Oxa-24-like (13.2%), Oxa-51-like (11.9%), Oxa-58-like (39.4%), Oxa-23-like (12.6%), imp (9.2%), cmlA (19%) and cat1 (8.6%) were respectively reported too. Also in this study Frequency of integrons class 1, 2, 3 were (100%), (28%), (6.6%) respectively. Conclusions: High prevalence of integrons among Acinetobater baumannii isolated from Isfahan hospitals indicate the importance role of integron classes in multidrug resistance. Considering the increasing pattern of MDR infections is one of the important issues of treatment which can be effective strategy for curing.