We developed dinoflagellate-specific 18S rRNA gene primers. PCR amplification using these oligonucleotides for a picoplanktonic DNA sample from Long Island Sound yielded 24 clones, and all but one of these clones were dinoflagellates primarily belonging to undescribed and Amoebophrya-like lineages. These results highlight the need for a systematic investigation of picodinoflagellate diversity in both coastal and oceanic ecosystems.Dinoflagellates have received considerable attention due to their ecological and economical significance and their remarkable cytological and genetic features (6,7,20). However, our knowledge of the species diversity of these organisms remains limited even though novel living (2,3,10,14) and fossil lineages (4, 19) have been discovered. Knowledge of the diversity of "small" dinoflagellates is particularly deficient. The recent discovery of ultraplanktonic (Ͻ5-m) and picoplanktonic (Ͻ3-m) dinoflagellates in Antarctica and the Pacific Ocean (13, 15), respectively, is the first demonstration of a rich biodiversity of small dinoflagellates that have escaped routine microscopic detection. A better understanding of dinoflagellate biodiversity requires targeted approaches, particularly for picoplanktonic species.Development of dinoflagellate-oriented primers. Based on a large database of nuclear small-subunit (18S) rRNA genes, we designed PCR primers that target dinoflagellates. A total of 140 18S rRNA gene sequences, including sequences from dinoflagellates, diatoms, chlorophytes, haptophytes, cryptophytes, and other algae, were obtained from GenBank and were aligned using ClustalW1.8; 11 of the dinoflagellate species were sequenced in this study (GenBank accession no. DQ388456 to DQ388466). Regions unique to dinoflagellates were used to design three forward and two reverse PCR primers (Table 1), which were paired with previously described eukaryotic 18S rRNA gene universal primers (22) for DNA amplification.The primers were tested with 33 genera of cultured dinoflagellates (35 species, including Oxyrrhis marina), as well as nine other taxa (Table 2). Algal cultures were grown in f/2 medium (28‰ or 15‰ salinity), cells were harvested, and DNA was purified as previously described (23). Briefly, after cell lysis in 1 ml DNA buffer (100 mM EDTA [pH 8.0], 0.5% sodium dodecyl sulfate, 200 g ml Ϫ1 proteinase K), DNA was purified using DNA Clean and Concentrator columns (Zymo Research, Orange, CA). With these DNA samples as templates, PCR was performed using five combinations of the primers, as follows: primers 18ScomF1 and Dino18SR1 (expected product size, 0.65 kb), primers 18ScomF1 and Dino18SR2 (0.92 kb), primers Dino18F1 and 18Scom R1 (1.60 kb), primers Dino18F2 and 18Scom R1 (0.92 kb), and primers Dino18F3 and 18S com R1 (0.90 kb). All primer sets except the Dino18SF2-18ScomR1 set exhibited specificity for dinoflagellate 18S rRNA genes, which allowed amplification from most taxa examined (Table 2). The only exceptions were O. marina (often referred to as an ancestral dinoflagellate [17] or a p...