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The gas shale in the Lower Silurian Longmaxi Formation contains a considerable amount of biogenic silica. Various originated silicas in shale, derived from different depositional environment, are commonly associated with different degrees of organic matter enrichment, resulting in different mechanical and physical properties of shale reservoirs. Thin section identification, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), total organic carbon (TOC) analysis, X-ray diffraction (XRD) analysis, and X-ray fluorescence (XRF) spectroscopy were used to investigate the Lower Silurian Longmaxi shale from Well Yuye 1 in southeastern Chongqing, China to obtain a better understanding of the origin of silica in the Longmaxi Shale. The results show ubiquitous cryptocrystalline silicas with poorly crystalline morphology, which differs from that of the detrital silica, authigenic silica, and hydrothermal silica, proving that the cryptocrystalline silicas may have a biogenic origin. Major element and mineral composition analysis indicate no correlations between K2O/Al2O3 and SiO2/Al2O3 and between illite and SiO2, and negative correlations between TiO2 and SiO2/Al2O3, between illite and quartz and excess Si, and between Al2O3 and excess Si, and all samples being located in the area of non-hydrothermal origin in the Al-Fe-Mn diagram, excluding silicas of terrigenous detrital origin, clay mineral transformed origin, and hydrothermal origin. Moreover, the fact that almost all samples plot above the illite Si/Al line in the cross-plot of Si versus Al and the mean values of Al/(Al + Fe + Mn) and Si/(Si + Al + Fe + Ca) are close to the values of biogenic silica prove that the silicas are primarily of biogenic origin. Positive correlations between TOC and quartz and excess Si and numerous siliceous organisms are observed, indicating that the silicas are associated with siliceous organisms. The postmortem siliceous organisms underwent silica diagenesis via a dissolution-precipitation mechanism following the sequence of opal-A → opal-CT → cryptocrystalline biogenic silica as the burial depth and temperature increased. [ABSTRACT FROM AUTHOR]