Despite being closely related to Fusarium graminearum, which has been extensively characterized in many countries around the world, the population biology of Fusarium pseudograminearum, the main causal agent of crown rot of wheat in Australia and many other wheat-growing regions, has been comparatively poorly studied to date. A simple sequence repeat analysis of 163 F. pseudograminearum isolates from three field sites in NSW, Australia identified 128 distinct multilocus genotypes. Observed genetic diversity within fields was high, whilst genetic variation between fields was low. Across all fields genetic linkage disequilibrium was detected, but of the three individual fields, only one also displayed linkage disequilibrium. These results indicate that the isolates obtained were part of the same, highly diverse, population. However, this population may not be freely interbreeding. Whilst isolation incidence of F. pseudograminearum was found to be spatially aggregated within fields, spatial aggregation of genotypes within fields was weak. The study suggests that processes influencing population dynamics may operate at a scale larger than the narrow geographical scale covered in the fields sampled.