Citrus chlorotic dwarf-associated virus (CCDaV) emerged in Turkey in the 1980s. It has just recently been identified and characterized. Studies concerning genetic diversity of CCDaV are very limited. This study was designed to undertake a molecular characterization of Turkish CCDaV isolates. In this study, twenty-three CCDaV isolates obtained from different citrus species within the Eastern Mediterranean Region of Turkey (in which the first CCDaV in the world was discovered) were used for molecular characterization based on coat protein (CP) genes of CCDaV isolates. For this purpose, the CP gene from CCDaV isolates was amplified and cloned. The cloned CP gene of CCDaV isolates was sequenced bidirectionally. The resulting sequences were assembled and deposited in Genbank. Similarity rates and phylogenetic relationships in Turkish CCDaV isolates, including the limited number of CCDaV isolates found in Genbank, were further researched. As a result of the multiple sequence analysis, it was determined that Turkish CCDaV isolates showed over 98% nucleotide- and amino acid-based similarities with each other and other worldwide CCDaV isolates. In addition, as a result of phylogenetic analyses, it was determined that Turkish and Chinese isolates had a tendency to split apart from each other based on geographic origin. However, it was shown that there were no phylogenetically specific clusters in the Turkish CCDaV isolates similar to the host citrus species.