The primary seasonal phytoplankton bloom in the equatorial Atlantic occurs in boreal summer in response to seasonal strengthening of zonal winds. However, the equatorial Atlantic also has a secondary bloom in late fall – early winter. This secondary bloom is weaker than the primary bloom by a factor of two, but is subject to year-to-year variability that is similar in magnitude. Here, observational evidence, including sea level and SeaWiFS-derived chlorophyll-a concentration, is used to examine several potential causes of this secondary bloom. The secondary bloom varies independently of blooms along the eastern coastal zones. Also, the secondary bloom has a relationship with the cessation of the Northwest African monsoon, which propotes the secondary seasonal strengthening of the trade winds. The variability of the secondary bloom results from perturbations in the depth of the thermocline induced by zonal wind anomalies in the western tropical Atlantic. These wind anomalies are correlated with mean sea level atmospheric pressure anomalies in the region of the northern subtropical high as well as over the Amazon.