Dear Emel Ören have you checked the quality of DNA of those samples that don't work? Have you considered the posibility that this marker don't work with some strain(s)?

Have you tested your DNA reproducibility with PCR of an internal gene?

Dear Emel Oren 

checke the quality of DNA

Thank you all. ITS1-4 worked just fine wt the samples that did not work with ISSR.