Detailed analyses of benthic foraminiferal fauna and planktonic foraminiferal stable carbon isotopes at IODP Site U1391 were performed to reconstruct orbital-scale variability in primary productivity off the Portuguese margin over the last 1.3 Myr. Q-mode factor analysis of benthic foraminiferal census data from the >250 mu m fraction reveals four assemblages, which is mainly controlled by the organic matter flux to the seafloor deriving from surface water productivity. The Sphaeroidina bulloides assemblage accounts for nearly half of the total variance, consisting of S. bulloides, the agglutinated taxa and Lenticulina as major components and Cibicidoides robertsonianus, Planulina ariminensis and Uvigerina peregrina parva as subsidiary species. Cibicidoides wuellerstorfi and Bulimina mexicana are important accessory species of the Cibicidoides pachyderma-dominated assemblage. The miliolids assemblage is dominated by miliolids and B. mexicana with Uvigerina mediterranea as the important associated species. The Praeglobobulimina ovata assemblage is represented by P. ovata along with Globobulimina affinis, Melonis pompiloides, Melonis barleeanum and U. peregrina parva as important accessory species. High productivity often occurs during the interglacial stages and is characterized by the S. bulloides assemblage with subsidiary P. ovata assemblage, while low productivity often occurs during the glacial stages and is marked by the miliolids assemblage and the C. pachyderma assemblage. In addition to the distinct glacial/interglacial variations, there is a long-term decreasing trend in primary productivity recorded by benthic foraminifera, which is supported by a broadly increasing trend in the sediment redness (a*). Continuous wavelet analysis of high productivity-related Factor 1 loading (the S. bulloides assemblage) suggests that variations in primary productivity have a middle Pleistocene transition (MPT)-related shift in cyclicity from the similar to 41-kyr dominant cycle prior to the MPT to the similar to 100-kyr dominant cycle after the MPT. Cross-spectral analyses between the Factor 1 loading record and delta O-18 of Globigerina bulloides reveal the control of global ice volume changes on primary productivity. The high coherency between the Factor 1 loading record and delta C-13 of G. bulloides on the glacial/interglacial timescale suggests that primary productivity off the Portuguese margin may be largely affected by nutrient availability which was related to the Iberian surface hydrographic changes associated with changes in global ice volume.