Anopheles darlingiis a major malaria vector in the Amazon region and, like other vectors, harbors a community of microorganisms with which it shares a network of interactions. Here, we describe the diversity and bacterial composition from the midguts and salivary glands of lab-reared and field-capturedAn. darlingiusing metagenome sequencing of the 16S rRNA gene. The libraries were built using the amplification of the region V3–V4 16S rRNA gene. The bacterial community from the salivary glands was more diverse and richer than the community from the midguts. However, the salivary glands and midguts only showed dissimilarities in beta diversity between lab-reared mosquitoes. Despite that, intra-variability was observed in the samples.AcinetobacterandPseudomonaswere dominant in the tissues of lab-reared mosquitoes. Sequences ofWolbachiaandAsaiawere both found in the tissue of lab-reared mosquitoes; however, onlyAsaiawas found in field-capturedAn. darlingi, but in low abundance. This is the first report on the characterization of microbiota composition from the salivary glands ofAn. darlingifrom lab-reared and field-captured individuals. This study can provide invaluable insights for future investigations regarding mosquito development and interaction between mosquito microbiota andPlasmodiumsp.