Enigmatic millimetre-scale micro-concretions with pseudocrystal faces and dominated by green clay minerals occur in unfossiliferous siliciclastic mudstone of the Lower Ordovician (479.0–466.0 Ma) Tonggao Formation, South China. The fossil-free mudstone unit is associated with local biodiversity decline. The mineralogy and mineral chemistry of these concretions were unknown previously, and this study comprises a preliminary investigation. The concretions are dominated by Fe-rich phyllosilicate minerals including glauconite and clinochlore, with minor quartz and traces of magnetite. The textural relations between the micro-concretions and the surrounding matrix, and the preservation of original mudstone laminations within the concretions, point to an origin during early diagenesis. The mineralogy and chemistry of these concretions are consistent with an origin in a restricted, hypersaline, relatively deep-water environment, in accordance with stratigraphical and paleonotological data. These micro-concretions provide clues for a stressed environment with poor water circulation and anomalies of salinity and oxygen.