Macroalgae are essential for the functioning of temperate marine ecosystems, but there is increasing evidence to suggest that their survival is under threat from diseases caused by microbial pathogens. Nautella italica R11, of the Alpha-Proteobacteria, and Aquimarina sp. AD1 and BL5, of the Bacteroidetes, have been recognised as etiological agents of bleaching disease in the model red alga, Delisea pulchra. However, there is a limited understanding surrounding the molecular mechanisms of pathogenesis in these phylogenetically diverse opportunistic pathogens. Using RNA-seq analysis, N. italica R11 exhibited a strong transcriptomic response to the presence of D. pulchra. In particular, functions related to central metabolism, carbohydrate metabolism and oxidative defences were found to be upregulated. Similarly, using a genomics approach, the Aquimarina strains were found to encode a high abundance of carbohydrate degrading enzymes and oxidative defence mechanisms suggesting a common role for these functions across algal pathogens. However, we also observed distinct differences between the strains, with virulence in N. italica R11 dependent on a LuxR-type transcriptional regulator. While in the Aquimarina strains, the presence of a type nine secretion system (T9SS) may facilitate the secretion of carbohydrate degrading enzymes which may result in disease symptoms. The outcome of this research reveals new functions important for the virulence of phylogenetically diverse algal pathogens and contributes to our greater understanding of the complex factors mitigating microbial diseases in macroalgae.