Primary pulmonary hypertension (PPH) consisting of hereditary pulmonary arterial hypertension and idiopathic pulmonary arterial hypertension is an obstructive pulmonary hypertension caused by primary pulmonary artery hyperplasia. Both environmental and genetic factors are involved in the pathogenesis of PPH. Genes associated with TGF-β signaling pathway including BMPR2, ALK1, ENG, SMAD8 and other genes including NFU1, CAV1, KCNK3 and TopBPl have been associated with PPH. In this review, the function and mechanism of the above genes in the pathogenesis PPH are summarized.