The bacterial microbiota of the mosquito influences numerous physiological processes of the host. As low-microbial-biomass ecosystems, mosquito tissues are prone to contamination from the laboratory environment and from reagents commonly used to isolate DNA from tissue samples. In this report, we analyzed nine 16S rRNA data sets, including new data obtained by us, to gain insight into the impact of potential contaminating sequences on the composition, diversity, and structure of the mosquito tissue microbial community. Using a clustering-free approach based on the relative abundance of amplicon sequence variants (ASVs) in tissue samples and negative controls, we identified candidate contaminating sequences that sometimes differed from, but were consistent with, results found using established methodologies. Some putative contaminating sequences belong to bacterial taxa previously identified as contaminants that are commonly found in metagenomic studies but that have also been identified as part of the mosquito core microbiota, with putative physiological relevance for the host. Using different relative abundance cutoffs, we show that contaminating sequences have a significant impact on tissue microbiota diversity and structure analysis.