The habenula plays an important role in brain reward circuitry and psychiatric conditions. While much work has been done on the function and structure of the habenula in animal models, in vivo imaging studies of the human habenula have been relatively scarce due to its small size, deep brain location, and lack of clear biomarkers for its heterogeneous substructure. In this paper, we report high-resolution (0.5x0.5x0.8 mm(3)) MRI of the human habenula with quantitative susceptibility mapping (QSM) at 3 T. By analyzing 48 scan datasets collected from 21 healthy subjects, we found that magnetic susceptibility contrast is highly non-uniform within the habenula and across the subjects. In particular, we observed high prevalence of elevated susceptibility in the posterior subregion of the habenula. Correlation analysis between the susceptibility and the effective transverse relaxation rate (R2*) indicated that localized susceptibility enhancement in the habenula is more associated with increased paramagnetic (such as iron) rather than decreased diamagnetic (such as myelin) sources. Our results suggest that high-resolution QSM could make a potentially useful tool for substructure-resolved in vivo habenula imaging, and provide a groundwork for the future development of magnetic susceptibility as a quantitative biomarker for human habenula studies.