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Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention and control strategies. Flat mites of the Brevipalpus genus include several crop pests and the systematics of these mites represents a challenge for acarologists. Many of the most economically important Brevipalpus species have repeatedly been inaccurately identified. Such problematic classification has been attributed to the likely occurrence of cryptic species in the genus. In this study, we used an integrative approach that combined molecular analyses, including sequence-based species delimitation, with detailed morphological identification using traits that have recently showed to be taxonomically informative. Sequences of mitochondrial cytochrome c oxidase subunit I (COI) were obtained from individuals collected from host plants belonging to 14 genera and 13 families across 29 locations in the Americas (Brazil, Chile, USA). The phylogenetic analyses included previously published Brevipalpus sequences from GenBank, and the final data set was classified into 44 haplotypes. Six putative species were recognised by COI-based species delimitation analysis, and morphological evidence supported each of these species. The integrative approach revealed the occurrence of cryptic species in the Brevipalpus genus and contributed to the clarification of previously noted incongruences. The results presented here allow for the evaluation of taxonomic characteristics in a phylogenetic context and indicate new characters for the differentiation of Brevipalpus species. In addition, Brevipalpus incognitus n. sp. Ferragut & Navia, a cryptic species detected in this study, is described based on morphological and molecular traits. Implications of the advances in Brevipalpus systematics presented herein with respect to pest management are briefly discussed., We sincerely thank Dalva L. de Queiroz Santana, Embrapa Florestas, Colombo, Parana; Aloyseia Noronha, Eduardo Chumbinho de Andrade, Juliana Freitas-Astua and Francisco F. L. Barbosa, Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia; Alberto Luiz Marsaro Jr, Embrapa Roraima, Boa Vista, Roraima; Ricardo Adaime da Silva, Embrapa Amapa, Macapa, Amapa; Patricia Maria Drumond, Embrapa Acre, Rio Branco, Acre; Manoel Guedes C. Gondim Jr and Aleuny C. Reis, Universidade Federal Rural de Pernambuco, Recife, Pernambuco; Jose. C. M. Poderoso, Universidade Federal de Sergipe, Sao Cristovao, Sergipe, all from Brazil; and Jose Carlos V. Rodrigues, University of Puerto Rico, San Juan, Puerto Rico, for their help with sampling; Tatiane G. C. M. Galasso, Brazil, for help with extensive laboratory work. We also thank Maries Pages and Fabien Condamine, INRA, UMR CBGP, France, for their help concerning the Pons analysis. This study was funded by Brazil - National Council for Scientific and Technological Development (CNPq) (call CNPq/MAPA/SDA No 064/2008, grant 578353/2008-3), Embrapa Macroprograma 3 and Fundacao de Apoio a Pesquisa do Distrito Federal (FAP-DF). Authors DN and RSM are also grateful to CNPq for the research and pos-doc fellowships, respectively.