Our study investigated the type of acquired metallo-β-lactamases (MBLs) produced by carbapenem-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter baumannii from five hospitals in Iasi, Romania and the genetic relatedness of the strains carrying MBL genes. Of 106 carbapenem-resistant strains, 50 were positive for MBL production after screening with Etest MBL. PCR analysis showed that 46 isolates (44 P. aeruginosa and 2 A. baumannii) carried a blaVIM gene. By DNA sequencing we identified two class 1 integrons carrying the blaVIM gene in the P. aeruginosa: IntI1-aacA7-blaVIM-2-qacE∆1 in 43 strains, and IntI1-aacA7-∆blaVIM-∆cmlA1-qacE∆1 in one strain. In A. baumannii isolates the blaVIM-2 gene was not associated with a class 1 integron. Random amplified polymorphic DNA typing of VIM-2-producing P. aeruginosa strains revealed the presence of a major RAPD type in all five hospitals. Early detection and surveillance of such strains must be accompanied by rigorous infection control measures in order to limit the spread of MBLs in our clinical settings.