Since associations between genetic markers and quantitative traits were first reported (Sax 1923), much attention has been given to the potential uses of markers in breeding programs. A DNA molecular marker is an identifier (sometimes called a "tag" or "flag") of a particular genotype variant in the DNA sequence. Compared to morphological and biochemical markers representing phenotypic and biochemical variations (e. g., flower color, flowering time, seed size, seed coat color and sugar content), DNA molecular markers have several advantages: 1) not subject to environmental influence and usually more objective; 2) widely distributed in the whole genome; 3) can be detected in any stages of life including early growth stages of plants; 4) more abundant and less expensive than morphological markers, especially when they can be genotyped in high-throughput, which is greatly facilitated by the next-generation sequencing technologies. Molecular markers have been widely used to study genetic diversity, decipher evolution and phylogenetic relationships, characterize inheritance of plant traits, and assist in selective breeding in switchgrass.