Cyanobacteria are one of the major groups of algae causing algal blooms. In this study, we developed a rapid method for detecting Cyanobacteria using a recombinase polymerase amplification (RPA) method coupled with lateral flow (LF) strips. After releasing cyanobacterial DNA from cells using a freeze-cracking method, DNA was amplified using the RPA method. Next, the RPA products were detected using the LF test. LF-RPA successfully amplified the DNA of eight cyanobacterial species and detected their presence in the sample with high specificity, distinguishing them from five non-cyanobacterial species. The method could detect cyanobacterial DNA in water samples containing as low as 0.01 cell/mL Cyanobacteria, making the method more sensitive than polymerase chain reaction (PCR), which required cell densities of at least 104 cell/mL. LF-RPA could amplify and detect cyanobacterial DNA at any temperature in the range 30–45 °C in just 30 min and without the need for a thermal cycler. The method developed in this study is simple, rapid, and effective for on-site testing of Cyanobacteria, which may become a routine measurement in efforts to detect and treat harmful algal blooms.