Help of experts and special procedures, such as specific staining and electron microscopy, are often required for correct identification of ciliated protists. Here, we examined the potential use of combined morphological and molecular approaches for identifying marine benthic interstitial cilates. Sand samples were collected from Look-Lom Beach, Samaesarn Island, Chonburi Province during 2011-2012. Ciliates were extracted from the samples using seawater ice melting method. The organisms were then observed under a light compound microscope and some were cultured in an f/2-Si medium for further study. Forty six species of ciliates were encountered, namely Aspidisca sp., Blepharisma sp., Coleps pulcher, Coleps tesselatus, Coleps sp., Condylostoma arenarium, Condylostoma enigmatica, Diophrys sp., Euplotes sp. 1-3, Euplotidium sp., Frontonia sp., hypotrichs 01-05, karyorelicteans 01-16, Kentrophoros sp., Litonotus sp., Loxodes sp. 1-3, Loxophyllum sp., Mesodinium sp., Pleuronema sp., Protocruzia sp., Stichotricha sp., Uronema sp., and Uronychia sp. Clonal and pure cultures were successfully established for eight ciliate isolates belonging to three genera [i.e., Euplotes (2 isolates), Protocruzia (1), and Uronema (3)]. Five of these eight pure cultures [i.e., Euplotes and Uronema] were additionally investigated at molecular level. The PCR amplification and DNA sequencing with newly designed primers were performed to obtain ribosomal DNA (rDNA) sequences of the five ciliates, which cover small subunit (SSU) ribosomal DNA, internal transcribed spacer 1 (ITS1), 5.8S, internal transcribed spacer 2 (ITS2), and the first-1,300 bp of large subunit (LSU) ribosomal DNA. Sequence analysis of the partial LSU rDNA sequences showed number of nucleotide differences of 43 positions between two isolates of Euplotes spp. And nucleotide similarity of 100% among three isolates of Uronema. This result is consistent with examination based on light microscopy which suggests their anatomical differences for the former and their similar morphological features for the latter. Our study demonstrated the capability of using combination of morphological and molecular data for discriminating and classifying the marine interstitial ciliates. However, further study of additional ciliate samples and other regions of the rDNA gene should be conducted to ensure ultimate utilization of this combined approach.