Habitat loss and habitat fragmentation are amongst the major drivers of biodiversity loss globally. Although habitat fragmentation poses additional threats to biodiversity beyond habitat loss alone, the IUCN’s Red List of Ecosystems (RLE) does not provide guidance on how to assess these threats. This study develops an approach for incorporating habitat fragmentation into the RLE threat assessment and investigates additional insights such an analysis could provide beyond the analysis of distribution trends. This is achieved by quantifying RLE criteria A and B (distribution reduction, restricted distribution and decline) and comparing outcomes with indices of habitat fragmentation (core area, Largest Patch Index, Patch Cohesion Index and Aggregation Index) in the Cape Floristic Region of South Africa. Results revealed that much of the Cape Floristic Region is severely threatened by both landscape transformation and habitat fragmentation, but that treating the habitat fragmentation indices as additional RLE criteria did not alter the ecosystem threat assessment outcomes. Whilst this suggests that the existing RLE criteria implicitly account for habitat fragmentation, the relationship between fragmentation indices and RLE criteria were weak and highly variable in some cases, indicating that the RLE criteria alone do not sufficiently account for the threat of habitat fragmentation. Supplementing the RLE with habitat fragmentation measures highlights additional, unique information on threats to ecosystems. This simple approach has the potential to assist in setting conservation priorities and management goals, particularly in fragmented ecosystems.