The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid disorders characterized by ineffective hematopoiesis and increased risk of transformation to acute myelogenous leukemia (AML). The treatment of MDS is highly dependent on the reliability of the prognostic evaluation model. Current clinical prognostic scoring systems are comprised of morphology, pivotal clinical trials and cytogenetic findings. However, none of the available prognostic systems incorporates disease-related molecular abnormalities, such as somatic mutations. Cumulative evidence suggests that genomic data can also be used clinically to assist the diagnosis, prognosis, prediction of response to specific therapies, and the development of novel and accurate targeted therapies. Therefore, it is not possible to predict the response of patients to molecular targeted drugs, such as demethylation drugs. With the recent advance in whole- genome sequencing technologies, cumulative evidence suggests that genomic data can also be associated with the genesis, prognosis, prediction of response to specific therapies, and the development of novel accuvate targeted therapies, the issue of having some mechanism to dissect this heterogeneity and precision treatment is coming to the fore. However, there are still several hindrances to its clinical application. If these problems can be solved, molecular genetics will further provide a theoretical basis for the application of precision medicine in MDS.