We developed a MoS₂-coated mixed cellulose ester (MCE) membrane that significantly enhances both the efficiency and selectivity in capturing environmental DNA (eDNA). The MoS₂ coating facilitates preferential interactions with DNA via van der Waals forces between sulfur atoms in MoS₂ and the oxygen or nitrogen atoms in DNA bases. Laboratory and field tests with marine fish confirmed that the MoS₂-coated membrane significantly enhanced the selectivity and sensitivity of eDNA-based biota detection. This work represents the first application of a two-dimensional (2D) nanomaterial-based membrane for eDNA collection and detection. Furthermore, the membrane is low-cost, scalable, and requires no further processing. This invention offers a promising strategy for the development of 2D nanomaterials-based eDNA sampling tools and showcases their broader potential in environmental biotechnology applications.