Canine Adenovirus Type-1 (CAV-1) and Canine Adenovirus Type-2 (CAV-2) are causes of infectious canine hepatitis and infectious canine laryngotracheitis in both domestic and wild life, respectively. The epidemiology of the virus is not clear enough in the most territory. For this purpose, strains circulating in Turkey over a ten-year period were examined at the molecular level and a genetic heterogeneity was observed. In order to carry out this study, 32 fecal samples collected from shelter dogs with diarrhea in 2011 were used. Firstly, virus isolation was performed in MDCK cell line and cytopathogenic effects were observed in 4/32 samples. Secondly, four CPE-positive isolates were found positive for the E3 gene of CAV-2 by PCR. Strains obtained as a result of sequencing were placed on a different branch from other Turkish isolates under the same subgroup in the phylogenetic tree. According to partial E3 gene analysis, seven amino acid substitutions were detected between the strains. Due to Shannon entropy value and ConSurf analysis, it was determined that all amino acid changes occurred in important antigenic regions. This study pointed out the possible genetic heterogeneity among Turkish CAV-2 strains.