To isolate chl-DNA, you have to first Isolate intact chloroplast using percoll gradient from the leaves of your plant of interest, and then you can use any column based DNA isolation kit to isolate Chl-DNA. 

You can find a simple protocol ( Napier;s protocol) for chloroplast isolation in the link below : 

http://link.springer.com/protocol/10.1385/0-89603-321-X%3A355

I don't have any experience in isolating DNA from chloroplast  ,  if you want to  isolate chloroplast DNA  first  isolate chloroplast from plant cell than go for DNA isolation. I think this could work  .

Hello Nisma,

you can check the protocol described in this article: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084792

and in this book chapter: http://www.ableweb.org/volumes/vol-2/3-giebel.pdf

Hope this can help you.

Best,

Hello,

Such protocols are easy to find with a simple Google search :

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031468

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474675/

http://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_45-46/010008071.pdf

and so on. Good luck !

Thanks all of you for valuable suggestions and guidance. I'll check them out.

Hello!! I'd like to ask one thing. I have isolated Chloroplast from leaves with percoll gradient. Chloroplast, observed under a microscope were very beautiful. After I extracted DNA with a DNA extraction kit and amplified with chloroplast genes. I think that in my chloroplast DNA there was nucleus contamination... how can I obtain a Ch DNA without contaminations???