This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologies. Molecular techniques have also had critical roles in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. These techniques are well established and their advantages as well as limitations have been realized and described in this work. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. Some of the advanced marker techniques utilize newer classes of DNA elements, such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The most important and recent advances made in molecular marker techniques are discussed in this review, along with their applications, advantages and limitations applied to plant sciences.