An exquisitely preserved biota is preserved in the Pragian Rhynie cherts an ancient hot spring deposit located in NE Scotland. This biota inhabited the subaerial and subaqueous niches that developed on the distal parts of the outwash apron created by the silica depositing hot springs. A key element of the subaqueous biota preserved in the cherts is the charophyte alga Palaeonitella cranii (Kidston & Lang) Pia. With ecorticate thalli that give rise to whorls of furcating branchlets and anteridia that are attached to the branchlet furcations by a pedicel P. cranii has a body which is remarkably similar to that of the extant Nitelleae tribe of charophytes. Palaenitella has non-calcified gryogonites composed of 6 sinistrally spiralling cells to which are attached a single tier of 6 coronula cells, a form that has affinities with the extant Chareae tribe. Palaeonitella may, therefore, be an early ancestor of the Chareae, one that retains the body plan of the more basal Nitelleae. Overall, the preservation of biota in the Rhynie cherts is of a very high standard, but there are variations. Hiatuses in silica deposition may be recorded by the development of shrinkage textures, the experimental shrinkage of the Psilotum nudum, an extant analogue for the rhyniophytes, suggests that this texture records a hiatus that lasted a few weeks at most. Composite cherts mark the presence of longer hiatuses in silica deposition. In some cases silification was virtually instantaneous, indicating the presence of a silica gel. An abundance of organic matter in the small shallow freshwater pools was sufficient to lower the pH of silica-saturated waters with low salinity levels, enabling a silica gel to form instead of the precipitates of opal-A lepispheres that form more commonly.