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Organic matter is known to influence community composition and metabolism of marine prokaryotes. However, few studies have addressed this linkage in the deep ocean. We studied the relationship between fluorescent dissolved organic matter and prokaryotic community composition in meso- and bathypelagic water masses along a surface productivity gradient crossing the subtropical and tropical Atlantic Ocean. Four fluorescence components were identified, three humic-like and one protein-like. The distributions of the humic-like components were significantly explained by water mass mixing, apparent oxygen utilisation (AOU) and epipelagic productivity proxies in varying degrees, while the protein-like component was explained only by water mass mixing and epipelagic productivity. The diversity and taxonomic composition of the prokaryotic community differed between water masses: the Nitrosopumilales order dominated in water masses with high AOU and humic-like fluorescence (notably, the SubPolar Mode Water), and tended to co-occur with Marine Group II archaea, the SAR324 clade and Thiomicrospirales, while bathypelagic water masses displayed greater abundances of members of Marinimicrobia, SAR202 and SAR324. Water mass mixing regression models suggested that the distribution of some taxa (e.g., Marinimicrobia, SAR202) was dominated by mixing and selection within the water masses during ageing, while others (chiefly, Alteromonadales) were mostly influenced by local processes. Our results suggest a link between the composition of the prokaryotic community, oxygen utilisation and the signal of fluorescent dissolved organic matter, and has implications for our understanding of the processes that shape carbon cycling and prokaryotic communities in the deep ocean