Bedded chert is the only sediment type representative of the Paleozoic to early Mesozoic pelagic marine environment. Because of their association with ophiolites and island arc rocks, presence of datable microfossils and paleohorizontal reference provided by well-developed bedding surfaces, bedded chert sequences are often targeted for paleomagnetic tectonic studies. However, processes of magnetization acquisition in biosiliceous sediments, and consequently, the significance of their magnetic record, are not well understood. Our rock magnetic study of a Triassic–Jurassic radiolarian chert sequence, the Mino Terrane, Central Japan, shows that the ferrimagnetic assemblage of the gray chert units is of detrital origin, while the red chert's assemblage is dominated by authigenic phases – pigmentary hematite and biogenic magnetite – which contribute to the natural remanent magnetization. The presence of magnetofossils places red oxic chert in the category of prospective environmental archives. Magnetite-producing magnetotactic bacteria were apparently able to tolerate elevated concentrations of dissolved silica as well as a steep redox gradient in sedimentary pore-waters during the deposition of red chert layers. A strong uniaxial anisotropy due to chain-alignment of the biogenic magnetite grains likely contributes to the acquisition of anomalously stable partial thermoviscous magnetization by chert even at low metamorphic temperatures.