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Here we collate 173,333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys to long ocean voyages. This dataset concentrates on samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). Here we collate all available chlorophyll a data from Australian waters, gathered from researchers, students, government bodies, state agencies, councils and databases, along with the associated metadata. The Australian Chlorophyll a Database is available through the Australian Ocean Data Network portal (AODN: https://portal.aodn.org.au/), the main repository for marine data in Australia. The Australian Chlorophyll a Database will be maintained and updated through the CSIRO data centre, with periodic updates sent to the AODN. 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