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Harris County, Texas, remains at continuous risk to mosquito-borne diseases due to its geographic landscape and abundance of medically important mosquito vectors. Targeted mitigation of these mosquitoes requires accurate identification of these mosquitoes taxa. Currently, there is a paucity of genetic information to inform molecular identification and phylogenetic relationships beyond well-studied mosquito species. Here we utilized a genome skimming approach using shallow shot gun sequencing to generate data and assemble the mitochondrial genomes of 37 mosquito species collected in Harris County, Texas. This report includes the complete mitochondrial genome for 25 newly sequenced species spanning 10 genera; the genomes were consistent with reference genomes in the GenBank database having 37 genes (13 protein-coding, 2 rRNA and 22 tRNA), and average AT content of 78.74%. Bayesian and maximum likelihood tree topologies using just the easily aligned 13 concatenated protein coding genes confirmed phylogenetic placement of species for Aedes, Anopheles and Culex genera clustering in single clades as expected. Furthermore, this approach provided more robust phylogenetic placement/identity of study taxa when compared to the use of the traditional cytochrome oxidase I partial gene barcode sequence for molecular identification. This study demonstrates the utility of genome skimming as a cost-effective alternative approach to generate reference sequences for the validation of mosquito identification and taxonomic rectification, knowledge necessary for guiding targeted vector interventions.