Elucidating the transmission dynamics of mosquitoes, facilitating identification of non-invasive species, employing non-visual approaches for larval detection, and integrating next-generation surveillance techniques are pivotal for developing robust and sustainable strategies to prevent dengue and other mosquito-borne diseases. Illumina-based high-throughput sequencing was used to identify the presence of Aedes aegypti in dry and rainy seasons. The other identified mosquito species included Ae. albopictus, Culex pipiens, Cx. nigripalpus , and Armigeres subalbatus. To our knowledge, this represents the first comprehensive application of aquatic environmental DNA (eDNA) techniques to characterize mosquito biodiversity in Indonesia . The raw sequencing data generated in this study have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA1248132. These datasets provide a valuable reference framework for future eDNA-based surveillance efforts and quantitative assessments of mosquito populations in Indonesia’s aquatic habitats across different times and seasons. © 2026 The Authors.