It is a multilocus technique. Since no sequence data is required for designing primers. You can get a number of bands. I would suggest use gradient PCR for standardizing the annealing temperature.

Also it would be helpful if you provide information on what is your plant. I have worked with the UBC series.

Monisha Mitra Thanks Mam. I am working on different varieties of Lemon grass developed by my institute through clonal selection and recurrent breeding methods. I have not found any articles or solution on how to deal with non-specific amplifications in ISSR or any multi locus markers for that matter.

Note: I am using anchored ISSR primers for my experiments and I am using the annealing temperatures that were standardized and which were published in articles by my seniors. Still, are there any possibilities of getting Non-specific amplifications?

yes,

But sometimes matter experiment conditions so you check your experiment setup and regents and use a higher annealing temperature.