Background:Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technology (MALDI-TOF MS) isan innovative tool that has been shown to be effective for the identification of numerous arthropod groups includingmosquitoes. A critical step in the implementation of MALDI-TOF MS identification is the creation of spectra databases (DB)for the species of interest. Mosquito legs were the body part most frequently used to create identification DB. However,legs are one of the most fragile mosquito compartments, which can put identification at risk. Here, we assessed whethermosquito thoraxes could also be used as arelevant body part for mosquito speciesidentification using a MALDI-TOF MSbiotyping strategy; we propose a double DB query strategy to reinforce identification success.Methods:Thoraxes and legs from 91 mosquito specimens belonging to seven mosquito species collected in six localitiesfrom Guadeloupe, and two laboratory strains,Aedes aegyptiBORA andAedes albopictusMarseille, were dissected andanalyzed by MALDI-TOF MS. Molecular identification usingcox1 gene sequencing was also conducted on representativespecimens to confirm their identification.Results:MS profiles obtained with both thoraxes and legs were highly compartment-specific, species-specific andspecies-reproducible, allowing high identification scores (log-score values, LSVs) when queried against the in-house MSreference spectra DB (thorax LSVs range: 2.260–2.783, leg LSVs range: 2.132–2.753).Conclusions:Both thoraxes and legs could be used for a double DB query in order to reinforce the success and accuracyof MALDI-TOF MS identification.