Apical necrosis is a widely distributed disease in the culture of the marine agar-producing alga, Gracilariopsis lemaneiformis. In this study, 16 strains of epiphytic bacteria were isolated from the tip bleaching parts of G. lemaneiformis; of the 16 strains, two strains could induce healthy algal tips to become necrotic. They were identified as Thalassospira sp. and Vibrio parahaemolyticus by 16S rDNA sequence analysis and biochemical characterization. Using solid phase microextraction and gas chromatographymass spectrometry, the variation of volatile metabolites of G. lemaneiformis infected by these two strains of pathogenic bacteria was analyzed. The results showed that E-2-nonenal and 1-octen-3-one differed very significantly (P<0.01) between the Thalassospira infected group and the control group, while trichloromethane, 3-methyl butanal, benzaldehyde, and E-2-decenal differed significantly (P<0.05). The difference of 1-octen-3-one, benzaldehyde, and E-2-nonenal between the V. parahaemolyticus infected group and the control group was very significant (P<0.01), while 3-methyl butanal and octanal were significantly different (P<0.05). In conclusion, 1-octen-3-one, E-2-nonenal, and benzaldehyde might be the characteristic metabolites for the pathogenic infection and could be used as biomarkers for the disease prevention of G. lemaneiformis.