Diversity, Distribution, and Molecular Systematics of Octocorals (Coelenterata: Anthozoa) of the Penghu Archipelago, Taiwan Yehuda Benayahu 1, *, Leendert Pieter van Ofwegen 2 , Chang-feng Dai 3 , Ming-Shiou Jeng 4 , Keryea Soong 5 , Alex Shlagman 1 , Henryi J. Hsieh 6 , and Catherine S. McFadden 7 1 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv Univ., Ramat Aviv 69978, Israel 2 Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands 3 Institute of Oceanography, National Taiwan Univ., Taipei 106, Taiwan 4 Research Center for Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan 5 Institute of Marine Biology, National Sun Yat-sen Univ., Kaohsiung 804, Taiwan 6 Penghu Marine Biology Research Center, Fisheries Research Institute, Penghu 880, Taiwan 7 Department of Biology, Harvey Mudd College, Claremont, CA 91711-5990, USA (Accepted November 2, 2012) Yehuda Benayahu, Leendert Pieter van Ofwegen, Chang-feng Dai, Ming-Shiou Jeng, Keryea Soong, Alex Shlagman, Henryi J. Hsieh, and Catherine S. McFadden (2012) Diversity, distribution, and molecular systematics of octocorals (Coelenterata: Anthozoa) of the Penghu Archipelago, Taiwan. Zoological Studies 51(8): 1529-1548. The 1st ever surveys of octocorals in the Penghu Archipelago, Taiwan were conducted in 2006 and 2009. Scuba collections were carried out at 17 sites in northern, eastern, south-central, and southern parts of the archipelago. The collection, comprising about 250 specimens, yielded 34 species of the family Alcyoniidae belonging to Aldersladum, Cladiella, Klyxum, Lobophytum, Sarcophyton, and Sinularia. These include 6 new species that were recently described and another 15 records new to Taiwanese reefs. The northern collection sites featured a lower number of species compared to most of the central/southern or southern ones. To facilitate identifcation of octocoral species in future surveys, DNA sequences were obtained for the mitochondrial barcoding markers, COI and mtMutS, and for Cladiella and Klyxum only, nuclear 28S rDNA. These molecular markers reliably identifed specimens to genus and clade, but could not discriminate among species within some clades. Phylogenetic reconstructions based on the barcode markers revealed paraphyly among Cladiella, Klyxum, and Aldersladum, thus emphasizing the need for taxonomic revisions of these genera. These results highlight the importance of octocoral surveys to elucidate patterns of biodiversity and zoogeography in the East and South China Seas, including their marginal reef systems. http://zoolstud.sinica.edu.tw/Journals/51.8/1529.pdf Key words: Alcyonacea, Penghu, Taiwan, Species diversity. *To whom correspondence and reprint requests should be addressed. E-mail:yehudab@tauex.tau.ac.il T aiwan, a continental island with several offshore islets, is located at the junction of the Philippine-Japan island arc (Chen 1999), and features several well-developed coral communities at the northern edge of the South China Sea, particularly along its southern part and around offshore islands (Spalding et al. 2001). The occurrence of scleractinian corals in Taiwan is influenced by sea surface currents and seawater temperatures (Chen 1999). Some of the best- known and most-developed coral reefs of southern Taiwan are those of the Hengchun Peninsula, mainly at Nanwan Bay, Kenting National Park (Dai 1997). Scleractinian corals are well developed around the east-coast offshore islands of Green Is. ( Lutao in Chinese) and Orchid Is. (Lanyu in Zoological Studies 51(8): 1529-1548 (2012) 1529