Aragonite, a mineralogical constituent of speleothems in cave environments, is unstable and susceptible to inversion to calcite, a diagenetic process that involves changes in the mineralogy, texture and geochemistry of speleothems. However, the exact alterations of stable isotope compositions during such diagenesis have not been fully investigated. In this study, two aragonite stalagmites (SN3 and SN15) from the Shennong Cave, southeast China, were found partially inverted to calcite, as determined by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses, and thin-section inspections under microscope. The fiber relics and textural ghosts of aragonite preserved in coarse and equant mosaic calcite crystals clearly indicate that the calcite in these two stalagmites were inverted from aragonite. The stable isotope compositions (delta C-13 and delta O-18, given in per mil versus VPDB standard) of primary aragonite and secondary calcite were analyzed and compared, along both growth layers and growth axes. The results show that, along growth layers, differences of delta C-13 values between aragonite and calcite are negligible (0.1 parts per thousand-0.2%.), whereas differences of delta O-18 values between aragonite and calcite are significant (0.63 parts per thousand-0.87%0). Comparisons along growth axes show similar results: i.e., differences of delta 13C values are negligible (0.06% +/- 0.22%.) whereas differences of delta O-18 values are significant (0.85 parts per thousand +/- 0.29%.). Most likely, the aragonite in SN3 and SN15 were internally inverted by interactions of trace calcite crystallites and pore water within intercrystalline pore spaces, by a dissolution-reprecipitation process occurring in trapped pore water. In the case of the inversion of aragonite to calcite in speleothems, such as that observed in SN3 and SN15, the delta 13C values could be used in paleoclimate and paleoenvironment reconstructions because they are inherited from those of primary aragonite. Although the delta O-18 values might be cross-calibrated to those of primary aragonite if the aragonite-calcite fractionation offset is known (e.g., 0.85 parts per thousand +/- 0.29%0 in this study), however, the delta O-18 values of secondary calcite should be used with caution in such reconstructions as the delta O-18 offset value is not consistently invariable.