Delisea pulchra is a marine red macroalgae that is affected by a bleaching disease in the temperate East coast of Australia. Bacteria have been found before to be involved in the disease: bacterial community differences have been observed between healthy and diseased algae and two strains isolated from D. pulchra have been shown to cause the disease in vitro. In the current study we used deep Illumina sequencing which allowed us to detect both pathogenic strains in two natural occurring bleaching events and to show that one of the strains had a statistically significant higher abundance in bleached samples in comparison to healthy ones. The study also reveals yet-to-be-cultured potential pathogens and/or saprophytes that appear to participate in D. pulchra bleaching disease.