Abstract: Genomic sequencing studies have led to an increased understanding of the genotyping and molecular biology of pancreatic neuroendocrine neoplasias(pNENs). Recent studies reported that ATRX(α-thalassaemia/mental retardation syndrome X-linked)/DAXX(death-domain associated protein), ARID1A(AT-rich interactive domain-containing protein 1A, BAF250A), MUTYH(mutY homolog), and MEN-1(multiple endocrine neoplasia type 1) genes are remarkably mutated in non-functional pNENs, as well as genes encoding core components of the mammalian target of rapamycin (mTOR) signaling pathway. As a representative of functional pNENs, insulinomas had CNV amplifications and copy neutral with YY1 (Yin Yang 1) gene mutations. These mutated genes are involved in aberrations of chromatin remodeling, DNA damage repair, histone modification, and telomere maintenance, and thus might contribute to tumorigenesis and ultimately to the progression of pNENs characterized by divergent phenotypes. Differentiating genotypic subtypes of pNENs plays an important role in prognostication. Future therapies might be based on recent advances in molecular genotyping and mechanism.