Subterranean clover (Trifolium subterraneum L.) is an important pasture legume in many regions of Australia, and elsewhere. A survey was undertaken in 2014 to define the levels of soilborne disease and associated pathogens in annual subterranean clover pastures across southern Australia. Most of the 202 samples processed had very severe levels of taproot rot disease (disease index 60–80%) and extremely severe lateral root rot disease (disease index 80–100%). A complex of soilborne root pathogens including Aphanomyces trifolii, Phytophthora clandestina, and one or more of Pythium, Rhizoctonia and Fusarium spp. was found responsible for severe pre- and post-emergence damping-off and root disease. This is the first study to highlight the high incidence of A. trifolii across southern Australian pastures and the first to highlight the existence of natural synergistic associations in the field between Rhizoctonia and Pythium spp., Pythium and Fusarium spp., Pythium spp. and A. trifolii, and P. clandestina and A. trifolii. Nodulation was generally poor, mainly only in the 20–40% nodulation index range. There was no relationship between rainfall zone and tap or lateral root disease level, with root disease equally severe in lower (330 mm) and higher (1000 mm) rainfall zones. This dispels the previous belief that severe root disease in subterranean clover is an issue only in higher rainfall zones. Although overall the relationship between tap and lateral root disease was relatively weak, these two root-disease components were strongly positively expressed within each pathogen’s presence grouping, providing explanation for variability in this relationship across different field situations where soilborne root disease is a major problem. Most producers underestimated the levels and effect of root disease in their pastures. This study established that tap and lateral root diseases are widespread and severe, having devastating impact on the feed gap during autumn–early winter across southern Australia. Severe root disease was independent of the highly variable complex of soilborne pathogens associated with diseased roots, geographic location and rainfall zone. It is evident that soilborne root diseases are the primary factor responsible for widespread decline in subterranean clover productivity of pastures across southern Australia. Implications for disease management and options for extension are discussed.