Aphanizomenon is a genus of cyanobacteria that is filamentous and nitrogen-fixing and inhabits aquatic environments. This genus is known as one of the major producers of cyanotoxins that can affect water quality after the bloom period. In this study, an electrochemical aptasensor is demonstrated using a specific aptamer to detect Aphanizomenon sp. ULC602 for the rapid and sensitive detection of this bacterium. The principal operation of the generated aptasensor is based on the conformational change in the aptamer attached to the electrode surface in the presence of the target bacterium, resulting in a decrease in the current peak, which is measured by square-wave voltammetry (SWV). This aptasensor has a limit of detection (LOD) of OD750~0.3, with an extension to OD750~1.2 and a sensitivity of 456.8 μA·OD750−1·cm−2 without interference from other cyanobacteria. This is the first aptasensor studied that provides rapid detection to monitor the spread of this bacterium quickly in a targeted manner.