Isolates of Rhizoctonia solani were obtained from cotton seedling showing damping-off symptoms in Iran during 2007-2009. Characterization of various taxonomic groups was done using species-specific primers designed for conserved regions of ribosomal DNA internal transcribed spacer (rDNA-ITS) sequence and restriction fragment length polymorphism analysis of PCR-amplified rDNA-ITS region. Results revealed that from 168 isolates, 84 were AG4 HG-I, 35 were AG4 HG-II, and 49 were AG4 HG-III. All of the isolates were pathogenic on cotton and caused damping-off symptoms. Amplified fragment length polymorphism (AFLP) analyzes were used to investigate genetic structure of the pathogen populations collected from various geographic regions in different years. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 489 monomorphic and polymorphic bands generated with seven primer combinations, was performed. The resulted grouping of the isolates revealed 4 separate AFLP groups among a total of 168 isolates, which typically showed more than 86% fingerprint similarity. Isolates of the three different intraspecific groups of R. solani AG4 were clearly separated in the dengrogram obtained from AFLP data. Within each AFLP group, two or more haplotypes were detected with a genetic similarity of 100%. Analysis of Molecular Variance (AMOVA) revealed that geographic region was the dominant factor determining genetic structure of R. solani AG4 populations; but year of sampling had not significant effect.

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