The giant Bayan Obo REE deposit bears a large amount of iron resources as well. However, the genesis of iron mineralization is still highly controversial with limited research. In this study, new data of trace elements of magnetite from Bayan Obo ores, Eastern contact zone skarn and Heinaobao BIF are obtained by Laser ablation (LA) ICP-MS analyses, revealing the genesis of Bayan Obo iron resources through comparing study. The Bayan Obo deposit contains disseminated, banded and massive ores, and in which magnetite is associated with REE minerals, fluorite, aegirine, riebeckite, and biotite. Euhedral magnetite in the skarn of Eastern contact zone is usually associated with pyrite, biotite, fluorite, and bastnaesite. There are two types of magnetite in the Heinaobao BIF: (1) euhedral to subhedral magnetite associated with quartz and a small amount of amphibole; (2) anhedral magnetite associated with quartz, garnet, plagioclase, amphibole and biotite.Magnetite in the Bayan Obo is enriched in Ni, but depleted in Mg, Al, Ti, Ge, Mn, Ga and Zn, showing low and variable concentrations, which is similar to the hydrothermal magnetite. The contents of some trace elements (e.g. Ti, Mn, Sc, Zn, Nb and REE) of magnetite from the skarn ores are generally higher, indicating a relatively high formation temperature. Magnetite in the Heinaobao BIF is generally characterized by low and uniform trace element contents, except for the abnormal values of Ti, Al, Cr and Mn, suggesting the involvement of terrigenous clastic materials. Compared with Bayan Obo magnetite, the skarn magnetite has the highest Sn/Ga, Co/Ni, Nb/Ta, La/Yb, Ti/V and Ti/Al ratios, while magnetite in the BIF has the highest Al/Co and lowest Nb/Ta ratios. The significant difference in mineralogical and trace element characteristics among the three types of magnetite indicates that the iron resources in Bayan Obo deposit are unlikely to be a skarn Fe deposit nor a BIF deposit. However, the Bayan Obo magnetite shows similar geochemical characteristics to hydrothermal magnetite related to carbonatite, both of which are depleted in high field strength elements, such as Zr, Hf and Ta, and show strong positive anomalies of Mn and Zn and negative anomalies of Co and Ga. In addition, in the diagrams of Ti vs. Nb + Ta and Ti vs. Zr + Hf, the Bayan Obo magnetite falls into the field of hydrothermal magnetite associated with carbonatite. In conclusion, it is recommended that the Bayan Obo iron deposit is a typical hydrothermal deposit related to carbonatite. In this contribution, the skarn magnetite formed at high temperature and the BIF magnetite was contaminated by terrigenous materials deviating from the expected region in discriminant diagrams. It is therefore proposed that the validity of these diagrams depends on a full understanding of mineralogical characteristics of samples and magnetite precipitation environment, and that multiple discrimination diagrams should be used in combination.