Phaeomoniella chlamydospora, (Chaetothyriales, Herpotrichiellaceae) is one of the main causal agents of Petri disease and esca on grapevines. We have used AFLP markers to study the population genetic structure of 74 isolates collected at different spatial scales: 56 isolates originated from vines with esca disease sampled from four French vineyards (Poitou-Charentes, Aquitaine, Languedoc-Roussillon, Alsace); 18 isolates were collected from a single plot (Aquitaine vineyard). Significant linkage disequilibrium indicated that P. chlamydospora populations are not panmictic, whereas the level of haplotypic diversity observed, 72 single multilocus haplotypes identified in total among the 74 isolates analysed, suggest that reproduction in this species may not be strictly clonal. Clustering analyses suggests the presence of two genetically differentiated but sympatric clusters of isolates. The level of differentiation between the two clusters is high (F ST = 0.23) and significant at 13 out of the 21 loci analyzed. The most plausible explanation for this pattern of admixture is the coexistence in P. chlamydospora French populations of two predominant clonal lineages. Finally, the low level of spatial genetic differentiation in this study is consistent with the spread of this fungus through the transport of infected plant material by human activities.