This protocol details the collection, filtering, and preservation of algae samples for DNA sequencing. Using 47mm Whatman/Swinnex filter holders or a filter funnel with 0.45µm cellulose nitrate filters, algae are captured from a homogenized bioassessment sample. The filtered algae are placed in screw cap tubes with a preservation solution, labeled, and stored at -20°C or -80°C for up to six months. Field blanks are collected by filtering deionized water. Sterilization of equipment is essential to prevent cross-contamination. This protocol ensures reliable algae sample collection and preservation for DNA analysis.