This study aimed to characterise the microbiomes in surface mucous from PAC and CCA (crustose coralline algae) from shallow reefs around St. John, US Virgin Islands. Using Illumina MiSeq high-throughput sequencing, we analysed 16S rRNA amplicon libraries of biofilms associated with each algal crust. Using additional algal marker genes (large subunit [LSU] rRNA and psbA protein D1 gene [which comprises part of the reaction center of photosystem II]), we definitively identified the algal species comprising PAC aggressively overgrowing shallow reefs in St. John.