Applications of molecular markers include but are not limited to: 

Gene mapping: Molecular markers are used to map the position of linked genes on chromosomes, aiding in understanding inheritance patterns. 

DNA fingerprinting and forensic analysis: Molecular markers play a key role in comparing DNA samples and determining their likelihood of similarity, which is crucial in forensic investigations and paternity testing

Identification of disease-resistance genes: Identified markers, which represent inherited traits, can be converted into simple, user-friendly protocols and validated across various genetic backgrounds to help in detecting diseases 

Genetic linkage mapping: Genetic maps can be constructed by calculating recombination frequencies between pairs of molecular markers

Disease identification: Molecular markers are used to detect genetic oddities or alterations in DNA sequences in order to identify genes associated with genetic disorders. 

Plant breeding experiments: DNA markers are used to determine genetic diversity, analyze somaclonal variations, and detect the proximity of cultivars and for phylogenetic analysis. 

Population Studies: Monitoring allele frequencies facilitates the study of population genetics, migration, selection, and diversity in ecological and anthropological research.