Molecular characterisations of genotypes give precise information about the extent of genetic diversity, which assists in the development of an appropriate rice breeding programme. The latest approach in plant biotechnology and molecular breeding, which is the development of the polymerase chain reaction (PCR) for amplifying DNA, DNA sequencing and data analysis, is an effective technique that can be used for the screening, characterisation and evaluation of genetic diversity. Traits that serve as genetic markers are by definition polymorphic; the more polymorphic the trait, the greater its potential value to germplasm management. The issue of homology may seem insignificant for morphological markers, but the increasing use of molecular markers has heightened its importance. Application of molecular markers is still prohibitively expensive for most large-scale applications in rice breeding programmes, where performance parameters such as yield, quality, disease resistance and other desirable growth characteristics are upgraded. Therefore, marker assisted selection (MAS) methods are currently used for more targeted applications in order to keep up with the rising demand for rice consumption. Since conventional breeding methods will not be able to meet the satisfactory harvest, the application of biotechnological tools is one plausible option to tap into the significant yield potential of rice.