The Zhenyuan orogenic gold deposit (>100 t Au), located in the northern part of the Ailaoshan shear zone (ASSZ) in South China, is characterized by extensive alteration and mineralization in a variety of host rocks. In the deposit, abundant Eocene lamprophyres have been infiltrated by ore fluids to produce carbonate veins with zones of disseminated fine-grained gold-bearing pyrite and arsenopyrite on both margins of the veins. Primary phlogopite, K-feldspar and magnetite have been altered to carbonate, sericite and fuchsite. Carbonate minerals and sericite in altered lamprophyre have higher Mg contents than in other host rocks, reflecting the primitive geochemistry of the lamprophyres. Since carbonatization is the primary alteration type in the lamprophyres, whose main primary components are low-Ca phlogopite and K-feldspar, the CaO content of the lamprophyres reflects their degree of alteration. As alteration increases, incompatible element ratios remain essentially constant whereas Sr is enriched with Ca. In addition, Au with Co, Ni, As, Ag, Sb, and Bi are enriched, reflecting the addition of these metal elements during alteration of the lamprophyres. Altered lamprophyres have slightly lower 143 Nd/ 144 Nd (t) (0.51240–0.51253) and substantially higher 87 Sr/ 86 Sr (t) (0.70716–0.71234) than unaltered or weakly-altered lamprophyres, indicative of crustal contamination. The auriferous ore-forming fluids are thus interpreted to have migrated upwards and interacted with the sedimentary host rocks before altering the lamprophyres. Lamprophyres commonly show a close spatial and commonly temporal association with orogenic gold deposits worldwide. At Zhenyuan, the lamprophyres shared a common deep source to the auriferous ore fluids but did not themselves contribute to this fluid or its gold content.