Vibrio cholerae and Vibrio mimicus have similar phenotypes and genomes making rapid differentiation of these two species difficult. The first standard multilocus sequence analysis (MLSA) scheme for the identification of these species is described. A collection of 45 representative isolates from different geographical regions and hosts was examined using segments of the housekeeping genes pyrH, recA and rpoA. Overall, the closest phylogenetic neighbours of these species were Vibrio furnissii and Vibrio fluvialis. V. cholerae and V. mimicus formed separate species clusters on the basis of each gene, suggesting that these genes are useful as identification markers. These species clusters arose by the accumulation of point mutations. The pyrH gene showed the highest resolution for differentiating V. cholerae and V. mimicus. The maximum interspecies pyrH gene sequence similarity was 91 %. Clearly, V. mimicus strains were more heterogeneous than V. cholerae strains at the three loci. It is suggested that vibrio species may be defined on the basis of MLSA data. A vibrio species was defined as a group of strains forming a monophyletic group on the basis of these loci and with an intraspecific sequence similarity of at least 95 %. V. cholerae and V. mimicus isolates can be readily identified through the open database resource 'The Taxonomy of Vibrios' (http://www.taxvibrio.lncc.br/).Vibrio cholerae, the causative agent of cholera, is a major pathogen worldwide, particularly in the developing world. Cholera killed at least 5000 people in 2006 in Angola and neighbouring countries (http://www.who.int/en/). V. cholerae can be classified into more than 200 serogroups, but only serogroups O1 and O139 have been responsible for epidemics of cholera (Hunter, 1997;Kay et al., 1994). The species Vibrio mimicus was first proposed to encompass biochemically atypical non-O1 V. cholerae isolates that were unable to utilize sucrose (Davis et al., 1981). Phenotypically, most of the features of V. mimicus are identical to those found in V. cholerae (Davis et al., 1981). A sucrose-negative strain of V. cholerae was identified during cholera epidemics (Desmarchelier & Reichelt, 1984;Ramos et al., 1997), making it difficult to differentiate these two species on this basis. Because V. cholerae and V. mimicus share nearly 100 % 16S rRNA gene sequence similarity and show around 80 % DNA-DNA relatedness, discriminating between these species remains a difficult task for taxonomists and clinicians (Thompson et al., 2003). In addition, both species may also share important virulence factors, such as ct and tcp genes (Boyd et al., 2000;O'Shea et al., 2004). V. mimicus has only been associated with small outbreaks or isolated cases of diarrhoea (Campos et al., 1996;Uchimura et al., 1993).Amplified Fragment Length Polymorphism (AFLP) has proved to be the most powerful taxonomic tool for discriminating species and strains of vibrios (Thompson et al., 2003(Thompson et al., , 2004. However, AFLP is not easily adaptable for use in an online electronic tax...