This paper deals with the study of the Late Permian coal deposits from Chongqing and south-eastern Hubei mining districts and of the Late Triassic coal deposits from Chongqing mining district. The Late Permian coals are characterized by relatively high amount of sulphide, sulphate and carbonate minerals and by a high total content of trace elements (with respect to the Late Triassic coals) due to the marine influence on the depositional environment. The Late Permian Chongqing and the southeastern Hubei coals showed similar geochemistry and mineralogy. However, there were some differences due to the different source rock and magmatic influence on Hubei coals. The concentrations of most trace elements in the Late Triassic coal were relatively low when compared with the usual range of the worldwide concentrations. By contrast, the contents of Ta, Se, Nb, Sc, Hf, Tl, Bi, Cu, V and Zn in the Late Permian Chongqing and Southeastern Hubei coals were higher than the usual range. Differences in occurrence of major and trace elements were found between Late Permian Hubei and Chongqing coals. Thus, most of the trace elements investigated presented an aluminosilicate association, followed by sulphide–arsenide (Fe, S, As, Pb, Mo, Ni and Co, in most cases) and carbonate (Ca and Mg) affinities in both areas. However, there was an important phosphate and zircon association in the Chongqing coal, whereas the carbonate association was significantly influenced by magma in the coals from Hubei. In the Late Triassic coal most of the major and trace elements investigated occur in aluminosilicate associations, with the exception of S, Fe, Ca, Mn, Sr, Sn, Ba, Nb, Mo, Mg, Co and Ta, with carbonate, sulphate and sulphide affinities.