Twenty-nine low sulfur coal samples were selected to determine the magnitude and variability of mercury (Hg) content in a well-documented stratigraphy system including ten continuous coal seams in Zhuji Coal Mine, Huainan Coalfield, Anhui Province, North China. Mercury content of samples was measured on a direct mercury analyzer and confident results were obtained as evaluated by standard references, sample replicates and procedural blanks. The calculated overall mine average Hg content is 71.19 ± 9.28 ng/g based on seam averages and weighting by the estimated reserve of each coal seam. The estimated Hg emission potential for Huainan coalfield is obviously lower than that calculated from coal emission factor in industrial use. An increasing trend of Hg content with the evolution of depositional environment was observed from Nos. 3 to 11-2 coal seams. Combining the evidence of sedimentology and paleontology, a better understanding was gained of the mechanism of Hg sequestration in specific coal benches. A large portion of Hg residing in the low sulfur coals presumably integrated to the functional groups of organic constitution, whereas pyrite was generally abundant in the high sulfur coals.