The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However how pathogens cause the disease and how the entire algal-associated community is involved in the process is unclear. To investigate this, here we perform a metagenomic analysis of microbial communities associated with diseased and healthy D. pulchra across multiple bleaching events. This allowed us to identify taxa and gene functions enriched in the microbial communities of bleached versus healthy algae.