A study was made on the incidence of Fusarium spp. associated with pods of annual Medicago species, in particular M. polymorpha var. brevispina, in Western Australia, including sites where either feed refusal or reduced feed intake by sheep had previously been reported. From a first series of 7 sites where M. polymorpha var. brevispina in particular, but also M. truncatula, were sampled, there was an extremely high incidence of F. acuminatum (83%) on pods at the Cunderdin site where feed refusal by sheep had been previously reported. There were high incidences of F. avenaceum on pods at Katanning (48–65%), but much lower incidences at Shackleton (7%), Merredin (5%), Kellerberrin (3%), and Cunderdin (1%). There was a high incidence of F. equiseti isolated from pods at Cunderdin (30%), but much lower incidences at Katanning (4–6%) and Shackleton (2%). F. chlamydosporum and F. graminearum were only isolated from pods at Cunderdin (14% and 9%, respectively). There were low incidences of F. oxysporum on pods at Katanning (2–4%) and Cunderdin (2%). In a second series of 15 randomly picked additional sites where only M. polymorpha var. brevispina pods were sampled, F. acuminatum was found at all 15 sites, with incidences ranging from 26 to 80% of pods carrying this fungus. F. avenaceum incidences were much lower (0–10%), but it was still recovered from 11 of the 15 sites. The incidences of other Fusarium spp. were generally low (0–6%, except for one case of 20%), and these were only isolated from 7 of the 15 sites. Our study is the first published report of Fusarium species associated with annual Medicago pods in Western Australia. F. acuminatum, F. avenaceum, F. equiseti, F. chlamydosporum, and F. graminearum have all previously been reported elsewhere to be toxigenic and one or more of these species may be associated with the sheep feed refusal and/or reduced feed intake situations observed in Western Australia.