Previous studies have evaluated the overall structure of populations of Fusarium pseudograminearum (teleomorph, Gibberella coronicola), causal agent of cereal crown rot, but there is no information available on spatial relationships of genetic variation in field populations. Three 1-m-row sections in crown-rot-affected wheat fields in the Australian grain belt were intensively sampled to estimate population genetic parameters and the spatial aggregation, or clustering, of disease aggregates and genotypes. Estimates of population genetic parameters based on amplified fragment length polymorphisms (AFLPs) indicated that the genetic diversity in isolates from the 1-m-row populations described a significant portion of the diversity recorded for corresponding field and regional populations. In point pattern analysis, there was physical clustering and aggregation of F. pseudograminearum isolates from two of the three sites. Analysis of the spatial distribution of clonal haplotypes (DICE similarity ≥ 97%) indicated significant aggregation of clones in all three 1-m-row populations. Based on matrix comparison tests, both mating types and genetic distances had significant spatial aggregation for at least two of the three 1-m-row populations. This is consistent with the presence of non-random spatial genetic structure due to clonal aggregation. High levels of genetic diversity and spatial structuring of disease and genotypes in at least two of the three 1-m-row populations is consistent with the hypothesis that stubble is a primary inoculum source in no-tillage farming systems, resulting in aggregated patterns of disease and allowing for haplotypes to be maintained in the field over a number of annual cropping cycles.