Water flooding phenomena in the cathode of direct methanol fuel cells were analyzed by using electrochemical impedance spectroscopy. Two kinds of commercial gas diffusion layers with different PTFE contents of 5 wt% (GDL A5) and 20 wt% (GDL B20) were used to investigate the water flooding under various operating conditions. Water flooding was divided into two types: catalyst flooding and backing flooding. The cathode impedance spectra of each gas diffusion layer was obtained and compared under the same conditions. The diameter of the capacitive semicircle became larger with increasing current density for both, and this increase was greater for GDL B20 than GDL A5. Catalyst flooding is dominant and backing flooding is negligible when the air flow rate is high and current density is low. An equivalent model was suggested and fitted to the experimental data. Parameters for catalyst flooding and backing flooding were individually obtained. The capacitance of the catalyst layer decreases as the air flow rate decreases when the catalyst flooding is dominant.