The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hampered by the lack of reliable, well-curated reference databases to which sequences recovered from the environment can be compared. The Protist Ribosomal Reference (PR2) database addresses this need by providing a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy from the domain level to the species level.