Rare marine microbial taxa play key ecological roles in the marine ecosystem however these roles are not well understood. In this study we analysed data from three moored National Reference Stations (NRS) of the Integrated Marine Observing System (IMOS): Maria Island, Port Hacking and North Stradbroke Island. Monthly water samples were collected from six depths for three years and used for Illumina (Mi/Seq) based bacterial and archeal 16S rRNA gene amplicon sequencing. Data is used to investigate microbial community composition of the rare taxa (abundances below 0.1% of total reads of all samples per station) and abundant taxa (abundances above 0.1% of this threshold). The rare microbial taxa of the three NRSs comprise approximately 98% of the total operational taxonomic units (OTUs). Rare and abundant taxa were classified as Persistent (>75%), Intermittent (25-75%) and Transient (<25%) based on their abundance across all samples. Overall results showed that at North Stradbroke Island and Port Hacking the rare taxa increase in abundance in deeper water samples compared with the surface samples. The rare biosphere showed different patterns in depth and seasons. During late winter at NSI at ~ 30m depth a drastic decrease of the abundant persistent OTUs was observed over two years, with a concomitant increase in the rare transient OTUs. Rare taxa can increase in abundance when environmental conditions are advantageous and can therefore fluctuate in abundance between the seasons. Further work will focus on exploring the data to determine if environmental factors correlate with the concomitant decrease of abundant taxa and increase of rare taxa. In addition, divining the seasonal patterns of the rare microbes and what their ecological role is.