To obtain insight in the relationship between the spatial distribution of organic-walled dinoflagellate cysts (dinocysts) and local environmental conditions, fifty-eight surface sediment samples from the coastal shelf off SW Africa were investigated on their dinocyst content with special focus on the two main river systems and the active upwelling that characterise this region. To avoid possible overprint by species-selective preservation, samples have been selected mainly from shelf sites where high sedimentation rates and/or low bottom water oxygen concentrations prevail. Multivariate ordination analyses have been carried out to investigate the relationship between the distribution patterns of individual species to environmental parameters of the upper water column and sediment transport processes. The main oceanographical variables at the surface (temperature, salinity, nutrients chlorophyll-a) in the region show onshore-offshore gradients. This pattern is reflected in the dinocyst associations with high relative abundances of heterotrophic dinocyst species in neritic regions characterised by high chlorophyll-aand low salinity conditions in surface waters. Phototrophic dinocyst species, notably Operculodinium centrocarpum, dominate in the more oceanic area. Differences in the distribution of phototrophic dinocyst species can be related to sea surface salinity and sea surface temperature gradients and to a lesser extent to chlorophyll-a concentrations. Apart from longitudinal gradients the dinocyst distribution clearly reflects regional environmental features. Six groups of species can be distinguished, characteristic for (1) coastal regions (cysts of Polykrikos kofoidii and Selenopemphix quanta), (2) the vicinity of active upwelling (Brigantedinium spp., Echinidinium aculeatum, Echinidinium spp. and Echinidinium transparantum), (3) river mouths (Lejeunecysta oliva, cysts of Protoperidinium americanum, Selenopemphix nephroides and Votadinium calvum), (4) slope and open ocean sediments (Dalella chathamense, Impagidinium patulum and Operculodinium centrocarpum, (5) the southern Benguela region (south of 24°S) (Spiniferites ramosus) and (6) the northern Benguela region (north of 24°S) (Nematosphaeropsis labyrinthus and Pyxidinopsis reticulata). No indication of overprint of the palaeo-ecological signal by lateral transport of allochthonous species could be observed. © 2007 Elsevier B.V. All rights reserved.