AbstractAim To determine the spatial relationship between areas where different frog breeding groups occur and elevated anthropogenic activities, and the conservation implications thereof.Location South Africa.Methods Data on frog distribution ranges for the southern African sub‐region were used to identify biogeographical areas within South Africa. A random draw technique was used to determine whether areas where different frog breeding groups occur were characterized by higher levels of anthropogenic threats than expected by chance. Four measures (human population density, percentage land transformation, percentage protected area and invasive alien plants richness) expected to reflect threats were analysed.Results Terrestrial‐breeders were more often spatially associated with areas of threat than expected by chance in three of the seven biogeographical regions examined with land transformation and invasive alien plant richness being most significant. The south central was the only region where terrestrial‐breeders were spatially congruent with protected areas. Areas where stream‐breeders occur were spatially congruent with anthropogenic threats (with alien plants being most consistent) in five of the seven regions examined while protected areas were well represented in four of the seven regions. Non‐significant results were found for permanent and temporary aquatic‐breeders at both the national and the biogeographical scale.Main conclusions By analysing data at the sub‐continental scale we were able to identify regional threats to amphibians traditionally classified at species‐specific scales. Our study recognized land transformation and alien invasive plants as significant threats to areas important for the long‐term breeding success of stream and terrestrial amphibians in South Africa. Areas where different breeding groups occur in the south‐western Cape showed the greatest spatial congruence with the threats examined. Areas where terrestrial breeding frogs occur are not well represented in the current conservation network. This has important implications in addressing the current status of threats on amphibians in a biogeographical context.