Animal husbandry is considered a substantial part of agriculture which is important for the economic development of a country. The local potential for the livestock sector has remarkably developed in the past few decades with the introduction of technological advancements. Identification and traceability of livestock populations evolved as critical points in the production chain. Molecular marker-based genetic studies have addressed the preliminary complications of the livestock field. The intended objective of genetic studies is to select and maintain superior traits which have a direct impact on economic value. In that regard, the application of genetic markers has a significant role. RFLP, SCAR, AFLP, SSR, ISSR, EST, RAPD, STR, SCoT, and STS markers are prominently used despite animal identification and traceability, determination of genetic distance, sex determination, parentage determination, genetic conservation, gene mapping approaches in the livestock field. The present review is a critical study of current molecular biological techniques and their versatile applications in animal identification and traceability approaches and possible improvements of the available techniques to address the major concerns in the field.