Single Nucleotide Polymorphism (SNP) is a DNA sequence variation caused by the mutation at the level of genomic nucleotides. It has been reported as the third generation of genetic markers. The SNP-arrays, based on the principle of SNP, plays an important role in disease research mainly for genomic detection of predisposing genes. As a convenient, confident, sensitive and efficient technique, SNP arrays could be applicable for the multiple-point interaction analysis of candidate genes, making it a promising and powerful method for DNA analysis. Hematological malignancies consist of various categories and their incidence is rising significantly. A multiple-point gene interaction has been reported as the essential pathogenetic mechanism of these diseases. This review illustrates the process of SNP-arrays in genome-wide assay and the application of this technique to the pathogenesis, clinical manifestation, therapeutic response and the prognosis of the hematological malignancies, including leukemia, malignant lymphoma, juvenile myelo-monocytic leukemia, myelodysplastic syndrome, multiple myeloma and so on.