The diversity of marine benthic interstitial ciliates in sand sediments sampled from Look-Lom Beach, Samaesarn Island, Chonburi Province were investigated during September 2011 to March 2013. Sixty morphospecies belonging to 27 genera were documented using light microscopy. Karyorelictean ciliates were the most abundant group and 24 morphospecies of them were recorded. Of all genera, eight, namely Epiclintes, Prodiscocephalus, Protocruzia, Remanella, Trachelocerca, Tracheloraphis and Urostyla, were reported for the first time in Thailand, suggesting unexplored diversity of meiofaunal ciliates. Amplification and sequencing of ribosomal DNA of about 3,000-3,500 bp were conducted for individually isolated ciliate cells. A total of 21 sequences derived from 14 species were obtained and used as molecular signatures for species identification of the examined taxa. Our study not only pioneers the application of molecular tools in taxonomic identification of marine benthic interstitial ciliates but also provides the first comprehensive data on their biodiversity and underpins the need for more intensive and extensive investigations into biodiversity of marine benthic protists in Thailand.