This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total 289 CO1 barcode sequences were obtained from 34 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analyzed by means of the Barcode Index Number (BIN) and the other tools available in BOLD system. Results showed that the knowledge of freshwater miolluscs diversity in the South Caucasus is far to be comprehensive. For the studied 34 morpho-species, 298 barcodes were clustered into 42 BINs from which unique BINs were defined for 14 species, and 6 species were characterized with more than a single BIN. From the studied taxa, 60% were characterized larger than 2.2% sequence divergence indicating the possibly high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the republic of Georgia (Galba schirazensis), and at least three undescribed species taxa belonging to genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasizing the need for further intensive morphological and molecular investigation of the South Caucasian freshwater molluscan taxa.