Deepanshu, ISSR, RAPD, AFLP give you anonymous DNA fragments often poorly reproducible, and fragments of similar size are not always similar in sequence.  RFLP has many other limitations (needs  more pure, large quantitaty of DNA, more labor). Barcoding, SSR, SNP are markers with known sequence and data can be compared between many experiments. It is better to use such markers. 

The other way to do that would be haplotyping the known varieties for cpDNA, using GBS (genetics-by-sequencing). This allows comparison of almost 30 markers, and with developed restriction - gives a nice overview across your sample collection.

I recommend you to use more specific DNA markers. 

Thanks all