Mudstone--the most abundant sedimentary rock type, composed primarily of clay- or silt-sized particles--contains most of the quartz found in sedimentary rocks. These quartz grains, which are chemically and mechanically resistant and therefore preserve their characteristics well, have long been considered to be derived from the continental crust. Here we analyse quartz silt from black shales in the eastern USA, dating back to the Late Devonian period (about 370 million years ago), using backscattered electron and cathodoluminescence imaging and measure oxygen isotopes with an ion probe. Our results indicate that up to 100% of the quartz silt in our samples does not originate from the continental crust. Instead, it appears to have precipitated early in diagenesis in algal cysts and other pore spaces, with silica derived from the dissolution of opaline skeletons of planktonic organisms, such as radiolaria and diatoms. Transformation of early diatoms into in situ quartz silt might explain the time gap between the earliest fossil occurrences of diatoms about 120 Myr ago and molecular evidence for a much earlier appearance between 266 or even 500 Myr ago. Moreover, if many other mudstone successions show similarly high proportions of in situ precipitated--rather than detrital--quartz silt, the sedimentary record in mudstones may have been misinterpreted in the past, with consequences for our estimates of palaeoproductivity as well as our perceptions of the dynamics and magnitude of global biogeochemical cycling of silica.