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Coccolithophore export fluxes were investigated via the analysis of sinking matter, obtained from Eastern Mediterranean time-series sediment traps moored in three open sites of the north-eastern Mediterranean Sea located in the Athos Basin of North Aegean (M2 site), Cretan Sea of South Aegean (M3 site) and at Ionian Sea (Nestor site). The aim of our study was to determine the spatial, temporal and seasonal variability in coccolithophore fluxes, as well as to estimate coccolith biogenic carbonate contribution to the sedimentation process. Data from an additional time-series sediment trap located in the southwestern Black Sea were also considered for the comparison of the oligotrophic Eastern Mediterranean setting with the eutrophic Black Sea. Coccolithophore fluxes revealed a highly seasonal pattern during February–March in the North Aegean (peak in late February 2015: 85.6 x 105 coccospheres m−2 day−1; 27.9 x 108 coccoliths m−2 day−1), during March–May in the Cretan Sea (peak in late March 2015: 33.7 x 105 coccospheres m−2 day−1; 19.5 x 108 coccoliths m−2 day−1) and during February–March and May–June in the Ionian Sea (peak in late May 2012: 14.3 x 105 coccospheres m−2 day−1; 1.53 x 108 coccoliths m−2 day−1). The recorded maxima coincide with low sea surface temperatures, increased precipitation and high PIC fluxes. Coccosphere fluxes were dominated by Emiliania huxleyi comprising ~70% of the total abundance, in the North Aegean and ~50% in the Cretan and Ionian Seas. Syracosphaera pulchra was also prominent in the study sites, where its abundance reached 14% in the North Aegean and ~10% in the Cretan and Ionian Seas respectively. Florisphaera profunda represented one of the major taxa in the coccolith fluxes of all three Eastern Mediterranean sites (~25% in North Aegean, ~20% in Cretan and Ionian Seas), while Algirosphaera robusta and Umbilicosphaera sibogae were the most abundant among the minor taxa. The North Aegean Sea exhibited a considerably higher coccolith flux when compared to other sediment traps due to the prominent seasonal peak of E. huxleyi during winter (February–March) (>95% of the total abundance). In contrast to the Eastern Mediterranean sediment traps, the time-series data from the Black Sea showed presence of monospecific E. huxleyi assemblage increasing its abundance during late September–November (max 320 x 105 coccospheres m−2 day−1; at least 7.79 x 108 coccoliths m−2 day−1, coccolith flux derived only from coccospheres converted to coccoliths). In the Eastern Mediterranean, biogenic carbonate fluxes followed the general pattern of the total mass flux in all investigated areas, with the Black Sea coccolithophore CaCO3 flux being the lowest due to low the E. huxleyi coccolith mass. Overall, in the North Aegean Sea, coccolithophore fluxes are strongly dependent on surface waters nutrients enrichment due to winter vertical water column mixing, riverine inputs and Black Sea water inflows, while the fertilization and/or formation of fast-sinking aggregates due to episodic dust input event are affecting the coccolithophore fluxes in the Cretan and Ionian Seas. The intercomparison of the coccolith export fluxes in the studied NE-SW mooring transects implies a north-south and east-west decreasing pattern, depending on the variable oceanographic regimes and the associated environmental factors controlling the investigated areas.