Seaweeds are ecologically and economically important organisms. However, with increasing environmental stress, disease in seaweeds is likely to become more frequent and/or severe, leading to a reduction of both wild and farmed populations. Delisea pulchra, a red seaweed residing in the subtidal regions of the south-eastern coast of Australia, suffers from a bleaching disease which is characterised by mid-thallus pigmentation loss. The disease is caused by high-temperature stress and the activities of opportunistic pathogens. Interestingly, a TDA-producing Phaeobacter sp. BS52 can contribute to disease resistance of D. pulchra by mitigating the pathogen-induced shifts in host-associated microbiota (i.e., preventing dysbiosis). Further, a phylogenetically closely related strain Phaeobacter sp. BS23, has neither protective nor pathogenic effects towards D. pulchra and did not prevent the pathogen-induced dysbiosis. These findings indicate that Phaeobacter spp. may have species- or strain-specific ecological roles in the bleaching disease of D. pulchra, but the functions underpinning this variation are currently unknown. Recently we sequenced and de novo assembled the whole genomes of protective BS52 and the commensals Phaeobacter spp. BS23 and BS34 in D. pulchra. Phylogenomic analysis designated the strains BS52 and BS23 to species Phaeobacter piscinae and BS34 to Phaeobacter inhibens. Using comparative genomic analysis, the study identified putative functions such as phage infection and antibiotic production that may contribute to the protective ability of BS52. The availability of high quality WGS supports the current and future studies looking into the genetics underpinning specific bacterial functions. This study highlights that subspecies level variations can lead to different disease protective effects in Phaeobacter spp. It is hoped that these findings will benefit future probiotics discovery and disease management in seaweeds with applications for conservation and aquaculture.