Pink berry microbial consortia are marine macroscopic microbial aggregates dominated by two sulfur cycling species. This study sequenced 184 independent, individual consortia with Illumina sequencing. Samples were collected between 2015 and 2017 in three salt marshes around Woods Hole (Falmouth, MA, USA): Little Sippewissett Salt Marsh, Great Sippewissett Salt Marsh and Penzance Point Salt Marsh. This study thus provides metagenomes from spatially distributed pink berry aggregates, covering the whole known geographic range of these consortia.