Almost my 70 samples worked just fine with ISSR (AG)8. However, the same condition did not work with other samples. My isolates are about trunk fungal diseases of almonds such as Neoscytalidium spp., Fusarium spp.
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)?