Abstract: Pea root rot, caused by Fusarium solani f. sp. pisi (Fsp), is one of the most important diseases on pea (Pisum sativum). Assessing the genetic diversity of the pathogen isolates from different geographical regions is crucially important for understanding of the genetic background of this pathogen and intelligently deploying host resistance. We screened SSRs in complete genome sequence of Nectria haematococca MPVI, and 107 SSR loci were selected for designing markers, from which 24 polymorphic primer pairs were developed. The 24 primer pairs were used to assess genetic diversity of 96 Fsp isolates from different geographical regions. Among 24 SSR markers, a total of 132 alleles were detected among the 96 Fsp isolates, the number of alleles for each of the loci ranged from 3 to 15 with an average of 5.5. The genetic diversity was estimated to range from 0.4855 to 0.8264 with the average value of 0.738. Using these markers, 93 genotypes were detected. When the genetic similarity coefficient was 0.8, 96 Fsp isolates were clustered into 10 groups by phylogenetic analysis. There was no correlation between SSR profile and either geographic origin or pathogenicity. Analysis of AMOVA revealed that variation mainly presented within Fsp populations (86.14%), and genetic differentiation of Fsp was significantly affected by geographical conditions and ecological environment.