To explore effective physiological indexes to distinguish the resistant lines and susceptible lines of Pyt hium porphyrae , the causal agent of red rot disease of Pyropia yezoensis , and establish the disease-resistance breeding strategy, we obtained and analyzed the candidate resistant and susceptible lines by population selection. Gametophytes of the candidate lines were cultured in seawater containing P yt . porphyrae zoospores. Antioxidase activities, including superoxide dismutase (SOD), peroxidase (POD) and polyphenol oxidase (PPO), were measured and compared between the two lines before and after infection. In the resistant lines, SOD and POD activities increased and then decreased, but PPO activity rose with the prolongation of the infection time. The phenylalanine ammonia lyase (PAL) activities also increased and then decreased after infection, but it had significantly different expression in the two lines without pathogen attack. The synthesis rates of β-1,3-glucanase, and cell-wall degrading enzyme were different from each other between the two lines after infection of P yt . porphyrae . Comparison in the contents of malondialdehyde (MDA) and reactive oxygen species (ROS) in the two lines showed that, the two contents varied synchronously in response to the pathogen attack. Changes of these enzymes activities or contents demonstrated that Pyr . yezoensis could resist against the pathogen of P yt . porphyrae with the antioxidant defense capacity. In addition, β -1.3-glucanase content showed extremely significant difference between the two lines, and the PAL had consistent expression difference. Therefore, phenylalanine ammonia lyase (PAL) and β-1,3-glucanase can be considered as an effective index to distinguish susceptible line and resistant line, with which the workload of the resistant breeding could be reduced in the future.