Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the digestive tract, and most of them are caused by the gene mutations of KIT or platelet-derived growth factor receptor α (PDGFRA). However, approximately 10% to 15% of the GISTs without KIT or PDGFRA gene mutations are called wild type GISTs, which include succinate dehydrogenase-deficient GISTs, BRAF mutant GISTs and neurofibromatosis 1-related GISTs. Researches on GISTs-associated genes can provide new ideas for the diagnosis and treatment of GISTs. The authors address the research progress of genes associated with the occurrence, development, diagnosis, treatment and prognosis of GISTs.