Understanding the factors that contribute to insecticide resistance is needed to mitigate its threat to vector control, particularly in Latin America, where vector control is being intensified as part of regional malaria elimination strategies. Next Generation sequencing has been applied to investigate the role of mosquito microbiota in various mosquito behaviors and functions. We report here for the first time the results of shotgun metagenomic DNA sequencing to characterize mosquito microbiota in relation to insecticide resistance phenotypes. Following evidence of a link between insecticide resistance and insecticide detoxifying endosymbionts such as Burkholderia sp. in stinkbugs, we hypothesized that the mosquito microbiota may contribute to insecticide resistance. Anopheles albimanus from northern Peru were sequenced using the Illumina MiSeq platform. Resulting data were quality checked using PRINSEQ and Trimmomatic quality control tools, and taxonomic composition analysis was performed using GOTTCHA, Kraken and MG-RAST. Similar to other mosquito species, our data showed that An. albimanus microbiota was dominated by a single taxon: Proteobacteria at the phylum level, and Enterobacter at the genus level. Up to 50 bacterial genera, including Burkholderia sp., constituted the remaining microbiota. Our ongoing analyses will further identify the core microbiota and their functions in insecticide resistant and susceptible strains of An. albimanus from Peru, Guatemala, and Mexico.