Abstract: Recently, the incidence of thyroid nodules has been annually increasing. High-resolution ultrasound and ultrasound-guided fine needle aspiration biopsy (FNAB) are the best means for preoperative diagnosis of thyroid nodules. However, the diagnosis of some nodules remains unclear. Hence, the use of FNAB bound to aspirate molecular markers in thyroid nodule has been developing rapidly. Currently, the major molecular markers studied are: mutations in BRAF and RAS genes, rearrangements in RET/PTC and PAX8/PPARγ genes; immunohistochemistry-based detection of galectin 3 (Gal-3), cytokeratin-19 (CK-19), human bone marrow endothelial cell-1 (HBME-1), etc. This review summarized the latest progress on molecular markers of fine needle aspiration biopsy of thyroid nodules.