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Background  Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 ( COI ) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on  COI  barcode, in order to establish a more reliable identification system for mosquito species found in Singapore.    Methods  We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for  Aedes, Anopheles, Culex  and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity.    Results  The  COI -based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report  COI  barcode sequences of 16 mosquito species which were not available previously in sequence databases.    Conclusions  Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore.  COI -based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-014-0569-4) contains supplementary material, which is available to authorized users.

DNA barcoding: complementing morphological identification of mosquito species in Singapore