depends on your evolutionary time scale....chloroplast genomics highly conserved across the species than mtDNA. if you need deeper phylogeny cpDNA fine but for recent divergence..i would go mtDNA

Dear Bihua Chen,

If you are willing to use only one marker, than I agree with Binod Regmi. But the best would be to sample both genomes, as well as the nuclear genome, to avoid making inferences only on a gene tree.

Hope this can help you.

I agree with Binod Regmi  and Manolo Perez. Are you constructing ancestral or recent phylogenies?

Dear Rafeal,

Yes

Hi Bihua Chen,

I think it depends on which group you are working on. For plants, the evolutionary rate of the mitochondria is very low, then the chloroplast genome might be a better choice. In addition, I agree with Manolo Perez, sample nuclear genome will avoid inappropriate interpretation based only on the cytoplasmic genomes. Hope this helps.

Xiangqin

Plant Mitochondrial DNA is still poorly understood and successful applications in plant phylogeny are rare (the amazing work on Amborella notwithstanding). Moreover, plant mitochondrial genes are actually more conserved than those in plastid DNA. Many molecular biologists who are not experienced in plants are not aware of the very different genetics of plant and vertebrate mitochondria. For the vast majority of questions I can imagine plastid DNA is the way to go if the alternative is mitochondrial DNA. I agree wholly with those respondents who caution the need to also consider nuclear markers.

Nuclear first choice, mtDNA second. If you have cpDNA use it, but in my opinion 3rd choice. Best use 3, or 2.

Both of them, but actual applicability depend on timescale you investigated. At the same time, any of them is not sufficient for reliable phylogenetic decisions without nuclear genes bring into study. 

Your question is Which one is suitable for phylogenetics study: mitochondria genomics or chloroplast genomics? That means your material is plant that's why chloroplast genome is in picture. For animals you can go with mtDNA without any hesitation but for plants, chloroplast genome is more reliable and more specific.

It will be a good starting point to apply the plant DNA barcodes in phylogenetic reconstruction, like ITS, matK, rbcL, trnL-F and psbA-trnH IGSs.

In my mind if you go for genomics why not use a shut gun approach in which you will be able to assemble both the plastid and the mitochondrial genomes... We are lacking thorough study comparing both genomes and this shotgun approach offer a great way to improve our knowledge on the concerted (or not) evolution of those two genomes. Moreover, it is also possible to assemble part of the nuclear genome with this approach (like the ribosomal operon) which allows to detect some phenomenon like hybridization or introgression.

I would recommend chloroplasts because plant mitochondria contain many repetitive and duplicated regions, what makes it more complicated to assemble. But you could use both indeed, a low coverage whole genome illumina run contains enough reads to assemble both genomes