Wheat (Triticum spp.) is a universally lucrative agricultural crop. An increase in wheat production has been shown through selection by the farmers which can increase the grain profitability. The determination of genetic associations among domestic cultivars is facilitated by molecular markers. Data on genetic polymorphism is valuable for the germplasm association and regarding the developing management strategies. The information would be supportive for potential genome mapping programs and for the relevance of intellectual property rights of wheat breeders. Present review is an effort for providing support information to wheat breeders to develop varieties with varied genetic environment to attain continuity in large-scale wheat production. In this review, we have tried to provide a collective depiction of relevant information about the usage of some commonly used markers in wheat. It may help researchers to find out the frequentness and application of different markers and compare their results. The manuscript may serve as a platform helping the intellectuals for the selection and modification of their marker system in wheat diversity analysis. The heart of this review is the emphasis on the performance of various molecular genetic markers in diversity studies in relation to definite approaches that are in practice since several years allied with the multifaceted wheat molecular breeding and its polyploid nature. © 2014 Springer Science+Business Media Dordrecht.