I used RAPD-PCR, also the sequencing of  ITS  (using ITS 1 and ITS4 primers) and IGS successfully with Fusarium moniliform  you can try it

Thanks Ayman, I am using  sequncing  the ITS  using ITS 1 and ITS4 primers, please if you have paper for how to measure the genetic diversity by using this method,

If you are interested in being able to compare your isolates to material that has already been identified, the most widely accepted gene in Fusarium is the translation elongation factor 1-alpha.  For widely used genes and genetic regions for Fusarium, see the Fusarium-ID website (http://isolate.fusariumdb.org/index.php).

Current recommendations for genetic diversity studies in Fusarium, and F. graminearum in particular, are to use several unlinked genes.  See some of the work by O'Donnell and/or Kistler, such as (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16643/),  (http://ac.els-cdn.com/S1087184508001849/1-s2.0-S1087184508001849-main.pdf?_tid=a0172590-1d85-11e4-98b5-00000aab0f6b&acdnat=1407342228_2477373c558666200fc9c2d5cbdde338), and (http://ac.els-cdn.com/S1087184507000515/1-s2.0-S1087184507000515-main.pdf?_tid=c874dce4-1d85-11e4-9613-00000aacb35f&acdnat=1407342295_64ce1c7a86899e71dba527090b8d0451).

I support the opinion of Linda Hanson: sequence of translation elongation factor 1-alpha and some more genes will give you more exact data and chance to compare your population to all GeneBank accessions. 

 You will not get much variation from ITS sequences. What you will expect to get among isolates would be >95% identities for ITS sequences. I would follow suggestion of Linda Hanson and generate sequence data for the recommended genes.

Our group have done similar work on rubber fungal pathogen - Corynespora casiicola. We isolated the ITS region from approximately 35 fungal strains and sequenced them.

Results of multiple alignment of approximately 550-600 bp ITS fragment from 35 isolates indicated sequence identity of more than 95%. We did not see much differences among the ITS sequences.

It is another proof that ITS sequences may not be suitable for differentiating closely related fungal isolates. Good luck...

I agree completely with the comments above - Linda Hanson mentioned very good and substantial references. May be it will be good to search acces to PubMed or Web of Science. Best success ! I agree that the ITS region will result in too many similarities.

Thanks for all comment , I do the ITS sequencing for Fusarium spp and the morphological characters say it is F. greamenarum but the ITS sequencing give me 99%  alignment with more then tow species of Fusarium , So now it change to use TEF gene to do the speciation for Fusarium  and i will see the result.