Within the regressive sequence (eustatic sea-level fall) that characterizes the French Southern Jura carbonate platform during the Kimmeridgian, a succession of three facies (called here units 1–3) may be observed in a palaeolagoon near Orbagnoux. Unit 1 is a shallow-water, intensely burrowed, carbonate deposit; unit 2 (consisting of laminated, organic matter-rich carbonate) represents a shallow lagoonal environment, prone to stromatolite development and organic matter accumulation; unit 3 consists of platy limestones almost devoid of identifiable biota. Trace element distributions indicate that depositional and early diagenetic conditions must have been reducing during deposition of unit 1 and, especially, unit 2, whereas they were much less reducing during deposition of unit 3. However, the latter does not contain body or trace fossils, with the exception of structures interpreted as calcified bacteria. The reasons why the apparently normal marine environment of unit 3 did not allow a normal biota to develop are explored and lead us to propose that: (i) unit 2 may be a Jurassic counterpart of modern kopara deposits (stromatolites of French Polynesian atolls); and (ii) unit 3 may be the result of palaeokopara reworking. This model invokes the extensive intervention of microbes in the formation of these carbonate deposits.