This study made use of distribution and abundance data of demersal fish and cephalopod species targeted during trawl surveys off Angola, Namibia and the west coast of South Africa, to determine species richness patterns including the location of diversity hotspots in the Benguela Current Large Marine Ecosystem. The reliability of alternative techniques for determining species richness patterns over the study domain, including geostatistical and non-geostatistical interpolation methods and regression type modelling, was tested using a cross-validation method. Generalized additive models were found to be the most effective method and were used to generate horizontal maps of species richness for different periods in each country. Despite changes in community structure that have been documented during the study period and which may be associated with climatic changes, this study showed the presence of consistently predictable hotspot areas over a 20–30-year study period (depending on country). The relationship between species richness and physical/environmental variables was inconsistent between countries, but generally hotspots of species richness were associated with greater depths and cooler bottom temperatures. Range shifts of species associated, for example, with warming of temperatures could conceivably affect the spatio-temporal persistence of hotspots in the long term.