Many native breeds are facing the problem of extinction. Therefore, urgently, genetic diversity of breeds must be studied and the results must be employed to find out the conservation priority of the breeds. Microsatellites and mtDNA sequences are the two types of genetic markers that have been found useful and have been employed widely in the studies revealing the genetic diversity of closely related populations. Studies based on these markers, in parallel to Archeological findings, indicated that the native Turkish cattle, goat and sheep breeds are close to one of the centers of domestication. Therefore, it is highly likely that these breeds are harboring potential genetic information to be utilized in the future. Hence, they must have high priority in conservation on the global scale. Again, genetic studies indicated that, morphological characters of the breeds may give incomplete/wrong information about the evolutionary history of the breeds. Furthermore, genetic studies indicated that, before the prioritization of the breeds in conservation, first the group of breeds having the same evolutionary history must be determined. For this, breeds must be examined with respect to several types of genetic markers, differing in their modes of inheritance. Recently, to determine the conservation priorities of the breeds, new methods, using various criteria, such as: genetic distinctness, genetic diversity level, adaptation to special environmental conditions, risk of extinction of the breed, are being developed. Yet, they are not fully developed. Lastly, it is well known that breeds loose genetic information as they go from one generation to the next. Simulation studies, give insights about how to minimize this inevitable genetic loss by using molecular markers. However, at the current stage of technology, employment of the emerging rules are very expensive.