Coccolithophores are calcifying phytoplankton and major contributors to both the organic and inorganic oceanic carbon pumps. Their export fluxes, species composition and seasonal patterns were determined in two sediment trap moorings in the open equatorial North Atlantic (M4 at 12° N 49° W and M2 at 14° N 37° W), which collected settling particles synchronously in successive 16-day intervals from October 2012 to November 2013, at 1200 m water depth. The two trap locations show a similar seasonal pattern in total coccolith export fluxes and a predominantly tropical coccolithophore settling assemblage throughout the monitored year. Species fluxes were yearlong dominated by lower photic zone (LPZ) taxa (Florisphaera profunda, Gladiolithus flabellatus), but also included upper photic zone (UPZ) taxa (Umbellosphaera spp., Rhabdosphaera spp., Umbilicosphaera spp., Helicosphaera spp.). The LPZ flora was most abundant during fall 2012, whereas the UPZ flora was more important during summer. In spite of these similarities, the western part of the study area produced persistently higher fluxes, averaging 241 × 107 coccoliths m−2 d−1 (117 × 107 to 423 × 107 coccoliths m−2 d−1) at station M4, compared to only 66 × 107 coccoliths m−2 d−1 (25 × 107 to 153 × 107 coccoliths m−2 d−1) at station M2. Higher fluxes at M4 were mainly produced by the LPZ species, although most UPZ species also contributed higher fluxes, reflecting enhanced productivity in the western equatorial North Atlantic. In addition, we found two marked flux peaks of the more opportunistic species Gephyrocapsa muellerae and Emiliania huxleyi indicating a fast response to nutrient-enrichment of the UPZ, probably by wind-forced mixing, whereas increased fluxes of G. oceanica and E. huxleyi in October/November 2013 coincided with the occurrence of Amazon River affected surface waters. Since the spring and fall events of 2013 were also accompanied by two dust flux peaks we propose a scenario where atmospheric dust also provided fertilizing nutrients to this area. Enhanced surface buoyancy associated to the river plume indicates that the Amazon acted not only as a nutrient source, but also as a surface density retainer for nutrients supplied from the atmosphere. Still, lower total coccolith fluxes during these events compared to the maxima recorded in November 2012 and July 2013 indicate that transient productivity by opportunistic species was less important than background tropical productivity in the equatorial North Atlantic. This study illustrates how two seemingly similar sites in an open-ocean tropical setting actually differ greatly in ecological and oceanographic terms, and provides valuable insights into the processes governing the ecological dynamics and the downward export of coccolithophores in the tropical North Atlantic.