The graphite in marbles from Oltrek, an uninhabited island on Lake Baikal, has been investigated by micro-Raman spectroscopy using visible and near-ultraviolet wavelength excitation. All graphite samples exhibit a sharp first-order Raman band at about 1,580 cm−1 with a width from 10 to 19 cm−1, and sometimes a D1 band with very low intensity, which is occasionally absent. Using Raman spectra data it was estimated that the temperature of graphite formation in the Oltrek marbles is about 530–650°C and possibly even higher. This evaluation is in good agreement with the temperatures (about 700°C) determined by a graphite isotope geothermometer of the graphite–calcite pair. Scanning electron microscopy images have recorded a сonical graphite morphology on the surface of plate crystals of graphite. Raman spectra of samples with cones about 200–400 nm sizes showed that the graphite was associated with nontronite in the specimens studied. Natural nontronite, a clay mineral of the smectite group, has not been well characterized using Raman spectroscopy. Here, the Raman spectra of the Oltrek nontronite were compared with the spectrum of nontronite from the weathered crust of the Salair Ridge, Russia. The formation of hexagonal–pyramidal structures on the surface of graphite with the participation of clay and bio-organic matter in marble is discussed.