Concepts, methods and applications of some of the most important molecular or DNA markers commonly used in plant science are presented here. General principles of molecular marker technology are explained with detailed descriptions of some of the notable basic concepts relevant to marker applications: Marker-assisted selection, quantitative trait locus analysis. The different types of markers used for these analyses described here are RAPD, RFLP, AFLP, ISSR, SSR, SNP, CAPS, SCAR and STS. These markers are used for chromosomal mapping using polymerase chain reaction (PCR). In addition, several salient properties of DNA markers were compared, and different marker systems included are PCR or non-PCR-based, dominant or co-dominant inheritance, locus-specific or non-specific, and levels of marker polymorphisms. It was classified on the basis of reproducible efficiency. Several molecular marker applications that have been recently employed to achieve various goals in plant research are also reviewed.