Certainly you can very well use cross-species SSRs for your work. Check the following article too.

Assessment of genetic diversity in the forest musk deer (Moschus berezovskii) using microsatellite and AFLP markers

http://download.springer.com/static/pdf/163/art%253A10.1007%252Fs11434-011-4572-2.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11434-011-4572-2&token2=exp=1485933377~acl=%2Fstatic%2Fpdf%2F163%2Fart%25253A10.1007%25252Fs11434-011-4572-2.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1007%252Fs11434-011-4572-2*~hmac=2ade965334444fe83f29d837cb450404c4f3dab9f220b1dc5109772a77d7ef88

Read the following you get solid idea about SSRs their origin, evolution and distribution etc. etc.

Origin, evolution and genome distribution of microsatellites

http://www.scielo.br/pdf/gmb/v29n2/a18v29n2.pdf

For ref. sake

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing (attached)

Thanks Dr. Yasin Jeshima Khan; I went through the article that you suggested which is very useful to get the idea.

I also like to thank Jetty Ramadevi for providing various the link and materials. I will go through them soon. Many thanks

yes you can

http://www.scielo.br/pdf/gmb/v29n2/a18v29n2.pdf

Hi Paras

You should be aware that cross-species SSRs many times have null alleles, and might suffer other amplification problems.

If you insist to use them, be sure to check the efficiency of your RT-PCR before going on.

Hope this helps

Pablo