A bacterium with potent agar-degrading capability was isolated from the surface of a red algae, Gracilaria tenuistipitata. Based on phenotypic characteristics, 16S rDNA gene sequence and a phylogenetic analysis, this bacterium was identified and named as Flammeovirga yaeyamensis strain YT. PCR using homology-based degenerate primers was employed to clone any agarase gene belonging to GH16 family encoded in F. yaeyamensis strain YT. The resolved 1512 nucleotides revealed that the cloned gene, namely AgaYT, encodes a protein of 503 amino acids comprising a signal peptide, a glycosyl hydrolase catalytic module and a C-terminal domain with an unknown function. The recombinant protein r-AgaYT is an endo-type beta-agarase hydrolyzing agarose to yield neoagarobiose and neoagarotetraose as the main hydrolytic products. The specific activity of r-AgaYT was determined about 178.6 U mg(-1) at 40 degrees C and pH 8.0. (C) 2011, The Society for Biotechnology, Japan. All rights reserved.