Silica stromatolites occur in a number of modern hydrothermal environments, but their formation in caves is very rare. The silica stromatolitic speleothems of the Branca Opala cave (Terceira Island, Azores), however, provide an excellent opportunity for their study. These formations may be analogous to ancient silica stromatolites seen around the world. Petrographic, mineralogical and geochemical analyses were undertaken on the silica speleothems of the above cave, and on the silica-tufa deposits outside it, with the aim of understanding their genesis. The possible hydrothermal origin of their silica is discussed. X-ray diffraction analyses showed opal-A to be the sole silica phase. Negligible ordering of this opal-A showed ageing to be insignificant, as expected for recent silica deposits. Most of the silica speleothems examined were definable as sub-aquatic opaline stromatolites that are not currently growing. Optical microscopy clearly revealed a lower microlaminated, an intermediate and an upper microlaminated zone within the stromatolites. Stromatolite types (I, II and III) were classified with respect to their internal structure and distribution throughout the cave. Scanning electron microscopy showed silicified bacterial filaments within the stromatolites, the silicified plant remains and the silica-tufa deposits. Bacteria therefore played a major role in the precipitation of the opal-A. Plasma emission/mass spectrometry showed major, minor and rare earth elements to be present in only small quantities. The rare earth elements were mainly hosted within volcanic grains. Rapid silica precipitation from highly super-saturated water would explain the intense silicification of the plant remains found inside and outside the cave. The opaline stromatolites, the silica-tufa deposits and the above-mentioned intense general silicification suggest a local hydrothermal source for the silica. Indeed, these deposits strongly resemble plant-rich silica sinter associated with low-temperature hot spring deposits that include bacterial filaments. However, no geochemical signals that might indicate a hydrothermal origin could be found.