I think it is possible...

Yes, it is very possible

sound novel and can be done. maybe the so called indigenous chickens have some DNA that is not consistent with what they are labelled locally.

For plants, there are some centers called 'germplasms' centers, which collects all kinds of 'germplasms' such as seeds etc. for a specific plant. Researchers can look for materials from those centers for marker study for different purposes, including phylogenetic studies. If you are interested in your proposed project on Zimbabwe's indigenous chickens, you need to know a way or a place ('center') where collects these chicken 'lines' for your experimental materials.

As an institution we are currently running a conservation program for these species we can collaborate.

I think it is possible. But, you have to have a marker strongly linked to trait/character of your interest. If such studies have not done yet, design an association mapping study. 

I was just speculating that due to the deleterious effects of climate change environmental stressors on livestock and poultry production, the indigenous chickens could play a major role especially in smallholder production systems as one of the mitigation strategies. \targeting improved production accompanied by conservation program for these species based on both genetics of adaptability and productivity through marker assisted selection, make the future planning and execution for developing strains which can withstand the unforeseen climate change but at the same time giving us a reasonable production.

The molecular markers  until now is a lab. approach , and lake confidence to be commercial  , I think that this process need more researches and techniques to be reliable and effective part in breeding . 

Through the idea that marker strongly linked to trait/character of your interest can be identified, can this not  be possible to use for selection purposes in indigenous chickens? The limitation in our third world countries might be the unavailability of molecular biology labs.

I think you need to get in touch with Dr Farai Muchadeyi at the Agricultural Research Council Of South Africa. She has done a lot of MAS for chickens. They also have the Illumina High throughput Infinium SNP chip, that you can use for genotyping your chickens. If you need me to facilitate that you get in touch with her, send me a message  with your contacts and i will email her. She will be glade to collaborate and help you out with your project. Right now her team is also doing something similar to chickens in SA.

Dear Never

The huge achievements in poultry industry ( in all world ) done with classical approaches of poultry breeding , selection and mating systems , I did not work against success of molecular genetics but this technique promise the world to do some things have economically worth value , when the molecular approaches become part of large scale poultry production , the breeding programs will be dramatically change .

Good Luck