In the dark regions of caves, the formation of stromatolites is virtually unknown. Although Mn oxide crusts presumably induced by bacteria have been described in some caves, they lack stromatolite features, and the evidence of microbial origin is normally inconclusive. Here we describe for the first time the occurrence of extensive Mn oxide stromatolites formed in the deep interior of a cave. The stromatolites are of decimeter thickness and kilometer extent and show features extremely similar to typical CaCO3 stromatolites. However, unlike most stromatolites, their biogenicity is supported by the exceptional abundance of fossil microbes. Our data support that the stromatolites were mainly induced by chemolithotrophic Mn-oxidizing microbes, and were formed in a low-gradient water-table stream passage at least ∼1 m.y. ago. The El Soplao stromatolites (Cantabria, Spain) may contribute to increasing our understanding of microbial life in extreme environments, as well as the role of bacteria in the genesis of modern and ancient Mn deposits.