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In the last few decades, Aedes albopictus (Skuse) (Diptera: Culicidae) (= Stegomyia albopicta), the so-called "Asian tiger mosquito", has spread from its native range in southeast Asia to Africa, the Middle East, Europe, the Americas, and Pacific islands. The spread of this species poses a risk to human health as it is considered to be one of the main vectors of dengue and other arboviruses. Aedes albopictus was reported in Croatia in 2004, thereafter it was discovered at several coastal localities in 2005 and to date it has spread to most coastal areas and islands in Croatia. Here we investigate the genetic variability of A. albopictus based on 39 individuals collected during the summer of 2009 along the East-Adriatic coast and islands of Croatia and Montenegro and using two mitochondrial molecular markers: cytochrome oxidase I (COI) and NADH dehydrogenase 5 (ND5). We identified a single ND5 haplotype, corresponding to the previously reported and worldwide-distributed haplotype H3. The COI marker was more variable and we identified four COI haplotypes. In order to identify the geographic origin of the populations that colonized Croatia, we performed phylogenetic analyses of ND5 and COI haplotypes in Croatian populations and other A. albopictus populations retrieved from the GenBank. The phylogenetic tree based on ND5 haplotypes revealed two well supported clades where the unique Croatian ND5 haplotype clustered with the majority of haplotypes originating from South-Asia, America, Europe, and Africa. Another smaller cluster consisted of only Brazilian haplotypes. The phylogenetic tree and haplotype network that resulted from the COI analysis also indicates that the three Croatian COI haplotypes cluster with European and American haplotypes. However the fourth Croatian COI haplotype was the only European haplotype that occurred in a separate clade (group) with Indian, South-Asian, and Brazilian haplotypes. This data suggests there have been several independent introduction events in Croatia.