Farm animals supply 30 percent of total human requirements for food and agriculture and 70 percent of the world’s rural population rely on livestock as a component of their livelihoods. On the basis of policy developments, climate change and diversifying market demands, livestock conservation practice is changing rapidly. Selective breeding and exchange of farm animals or germplasm among users within and across countries are most commonly used strategies of enhancing livestock production but it resulted in the reduction of the bio-diversity of breeds. The selection pressure strongly increased, and therefore the reproduction among breeds was seriously reduced, resulting in the fragmentation of the initial gene pool. The selection pressure further increased due to the use of artificial insemination, leading to a few industrial breeds with very high performances, but with low effective population sizes. Beside this performance improvement of industrial breeds, genetic resources are being lost specifically indigenous and local breeds, because of the replacement of traditional breeds by high performance industrial breeds at the worldwide level. Many breeds are already extinct, and genetic resources in indigenous cattle, sheep, and goats are thus highly endangered, particularly in developed countries. Based on sound genetic characterization, urgent conservation measures must be taken to avoid an irremediable loss of livestock genetic resources, integrating economical, sociological, and political parameters. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools to ensure that they are applied within the context of breed conservation as well as development. Recently, development of effective technologies opens new avenues for correctly characterizing the genetic resources, not only within the very diverse domestic breeds, but also in their wild relatives. In conclusion, genetic characterization of indigenous breeds of farm animals by the use of effective techniques and their conservation is only alternate to maintain farm animal bio-diversity.