This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the final one. Please cite this article as doi: 10.4081/jlimnol.2018.1746 Zooplankton baseline in a karstic system Faunistic survey of the zooplankton community in an oligotrophic sinkhole, Cenote Azul (Quintana Roo, Mexico), using different sampling methods, and documented with DNA barcodes Lucia MONTES-ORTIZ, Manuel ELÍAS-GUTIÉRREZ* El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal 77014, Quintana Roo, Mexico * Corresponding author: melias@ecosur.mx Key words: Barcoding; biomonitoring; inventory; light-trap; bioindicators. ABSTRACT This study is the first faunistic inventory of a zooplankton community from an open, karstic and oligotrophic aquatic sinkhole in the south of the Yucatan Peninsula (Mexico), we describe the richness of the zooplankton collected with the combination of plankton nets and light traps of our own design, using morphological and molecular characters to identify the species and demonstrate the effectiveness of only one set of primers to sequence all taxa. Recently, it has been demonstrated that different sampling methods can increase the number of zooplankton species from tropical and temperate systems dramatically. These more effective methods together with DNA barcoding can give a new and more realistic picture of the species dwelling in a freshwater system. In total, we sequenced 268 specimens, and the list of species known in this sinkhole increased from 13 to 77 taxa, with a projection of 87 in total, including cladocerans, copepods, ostracods, fish larvae, tadpoles, rotifers, chironomids, water mites, among others. From the 77 taxa identified by us, 72 BINS (Barcode Index Numbers, equivalent to putative species) were assigned by the BOLD Database (boldsystems.org), and 30 of them are new records for both, BOLD and GenBank (www.ncbi.nlm.nih.gov). There was an essential Accepted Article