Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization.