The development of DNA barcoding for species identification is a broad tool that has been emphasized in the recent decade. Since the 1980's, the increase of trade and exchange of goods has raised the number of invasive species reported. The new invaders are threatening the development of a sustainable agriculture, the preservation of natural habitats and raising the costs for urban landscaping. Molecular barcoding is part of an innovative approach to accurately identify and fingerprint life species. Barcoding methods are a valuable application for both pest ecology and biocontrol agents. Several universal mitochondrial and nuclear molecular markers of conservative regions such as Cytochrome Oxidase I (COI) and Internal transcribed spacer (ITS) have been used in barcoding for fingerprinting both pests and their natural enemies and have demonstrated high replication of results. Moreover, the development of new molecular markers targeting important arthropod and microorganism species has elucidated their taxonomic status. The objectives at the Center of Excellence for Quarantine and Invasive Species (CEQIS) laboratory are to generate and apply DNA barcoding tools and to build an integrative database of pests and beneficial organisms within the Caribbean and track their pathways. Current work at the laboratory addresses the identification of parasitoid communities associated to whiteflies in Solanaceae, Leguminosae and alternate host plants. Plant host species are also identified by both classic morphology and DNA barcoding. Barcoding clarifies discrepancies between morphological and molecular identification. Molecular approaches used clarify the taxonomy of the parasitoid complex associated to the Harrisia cactus mealybug, Hypogeococcus pungens. So far, other biological control agents have been targeted for barcoding at the CEQIS and include mites, coleopteran and coccinellid.