Background: In recent years, die-back of pistachio has become one of the most important diseases in Kerman gardens. With regard to the importance of this disease and the lack of comprehensive information regarding the population genetic structure of the pathogen, it is necessary to set an appropriate indicator in the study of genetic diversity.

Objectives: In the present study, we examined simple sequence repeats (SSRs) and restriction fragment length polymorphism (PCR-RFLPs) (two PCR-based marker assays) to determine Paecilomyces variotti genetic diversity.

Materials and Methods: The utility of SSRs and PCR-RFLPs was examined to determine genetic diversity using 20 isolates of Paecilomyces variotii. In order to determine the performance of indicators, effective multiplex ratio (EMR), polymorphism information content (PIC), and marker index (MI) were calculated.

Results: Both systems discriminated 20 isolates of P. variotii successfully but were different in the amount of detectable polymorphism. Using cluster analysis of digestion reaction, SSR based on UPGMA algorithm, and Jaccard similarity coefficient, the isolates with 70% similarity level were divided into 7 and 3 groups, respectively. Reviewed indicators were at higher level for PCR-RFLPs marker. Four restriction endonucleases enzymes in RFLP produced 20 loci that 90% of them were polymorphic; and for SSR it was 32 loci that 37.5% were polymorphic.

Conclusions: This is the first research in comparing two genetic marker systems in P. variotti. We were prompted to explore polymorphisms utility in P. variotti with a look at using germplasm screening mapping of genome and strain improvement programs.