The molecular epidemiology and the genetic basis of carbapenem resistance was investigated in 185 Acinetobacter baumannii isolates obtained from 13 centers of northern Croatia and Istria during 2009-2010. All isolates were multidrug-resistant, and 35 % (n = 64) were resistant to both imipenem and meropenem. ISAba1-driven overexpression of the intrinsic bla OXA-51-like gene was observed in all carbapenem resistant isolates, and 69 % of these (n = 44) also produced acquired OXA-type carbapenemases. The presence of bla OXA-58-like, bla OXA-24/40-like, and bla OXA-23-like genes was demonstrated in 33 % (n = 21), 27 % (n = 17) and 9 % (n = 6) of carbapenem-resistant isolates, respectively. None of the isolates harbored the bla IMP, bla VIM, bla SIM, bla NDM or bla PER β-lactamase genes, while bla TEM-1 was detected in five carbapenem- and ampicillin/sulbactam-resistant isolates. Sequence group determination showed a high prevalence (81 %) of isolates belonging to the International clonal lineage (ICL)-I, although the majority (80 %) of isolates carrying acquired carbapenemase genes belonged to the ICL-II. Random amplified polymorphic DNA analysis and multilocus-sequence typing of a subset of carbapenem-resistant isolates revealed a low degree of genetic variability within both ICL-I and ICL-II populations, irrespective of the genetic basis of carbapenem resistance. Overall, an increasing trend toward carbapenem resistance was observed for A. baumannii in Croatia, and the emergence of ICL-II strains producing a variety of acquired carbapenemases.