AimIt has been proposed that species diversity (SD) and genetic diversity (GD) co-vary across natural communities because both are shaped by processes such as immigration and drift. However, empirical reports are contradictory, and multispecies studies are rare. Here we test the hypothesis that the two diversity measures do not correlate in systems with high levels of immigration stochasticity and little GD caused by strong genetic drift.LocationTropical alpine habitats on six of the highest mountains in eastern Africa.TaxonVascular plants.MethodsWe sampled 375 taxa in 75 plots in five habitat types, recorded ecological variables, and genotyped 1793 plants representing 20 species/species complexes.ResultsWe confirmed that intrapopulation GD was exceptionally low in this system and found that most Species-Genetic Diversity Correlations (SGDCs) were weak and insignificant. Whereas SD was correlated with several environmental variables, GD was only correlated with mountain identity (geographical location) and mountain age.Main ConclusionsOur findings support the hypothesis that SGDCs are lacking in habitat island systems such as the tropical alpine region in Africa, which is characterised by frequent population size fluctuations, extinctions, and colonisations via long-distance dispersal (LDD) during the glacial cycles. The stochastic nature of LDD combined with strong genetic drift and founder effects is likely to cause low GD and lack of SGDCs, implying that SD cannot be used as a proxy for GD in conservation management of such systems.