Single nucleotide polymorphisms (SNPs) describe a change in a single nucleotide within the genome. SNPs are known as the markers of choice due to their desirable properties such as co-dominant in nature, robust, widely distributed throughout the genome, highly multiplexable, easily automated with high throughput techniques, have high reproducibility, and high efficiency for detection of polymorphism. Several studies have been successfully done for the identifications of the functional SNPs in the plant crops. However, the effects of the identified functional SNPs on plant phenotypes are not yet reviewed so far. Functional SNPs located in the coding regions of the gene can change the first or the second nucleotide sequence in the cordon which in turn alters the amino acid, its sequence, and protein structure that change the activities of the enzymes and finally results in the formation of new traits in the plants. The various desirable phenotypic variations produced within individuals of plant species include grain yields, quality traits, fruit size and shape, tolerance, resistance and adaptation to different abiotic and biotic factors, different colors of fruits and plants, flowering and ripening time. These important phenotypic traits could be improved through breeding using MAS. SNPs that are located in the coding sequence or found near to functional gene controlling desirable traits can help molecular breeder select targeted plant at the early growth stage. This makes the crop improvement program very efficient and rapid. Therefore, the application of marker technology particularly SNPs can increase the speed and efficiency of crop improvement. Therefore, the present seminar paper was targeted to review the application of SNPs in crop phenotypic traits.