Hi Santhosh...

ISSR is very well optimized DNA marker technology based on the microsatellite sequences....The ISSR primers are based on the microsatellites sequences and in addition they have 5-prime or 3-prime anchor sequences...Many ISSR primers are commercially available...However for organisms of your interest..I suggest you get information about the type of microsatellite sequences present in the genome and then select the sequences against which the primers can be designed....PCR conditions should not be a problem...you can use the published protocols with some optimizations..

Dear Kumar 

I hope this message finds you in good health and spirit.

In accordance with Ajay, it can be said that these type of markers are commercially available and you can use the published papers for your goal. Indeed, you can use the following server for design and develop other PCR-based markers.

http://batchprimer3.bioinformatics.ucdavis.edu/cgi-bin/batchprimer3/batchprimer3.cgi?PRIMER_TYPE=2&CLEAR_FORM=no&LOAD_EXAMPLE=no

All the best,

HR