Chalcedony is a spatial arrangement of hydroxylated nanometre-sized α-quartz (SiO2) crystallites that are often found in association with the silica mineral moganite (SiO2). A supplementary Raman band at 501 cm−1 in the chalcedony spectrum, attributed to moganite, has been used for the evaluation of the quartz/moganite ratio in silica rocks. Its frequency lies at 503 cm−1 in sedimentary chalcedony, representing a 2 cm−1 difference with its position in pure moganite. We present a study of the 503 cm−1 band’s behaviour upon heat treatment, showing its gradual disappearance upon heating to temperatures above 300 °C. Infrared spectroscopic measurements of the silanole (SiOH) content in the samples as a function of annealing temperature show a good correlation between the disappearance of the 503 cm−1 Raman band and the decrease of structural hydroxyl. Thermogravimetric analyses reveal a significant weight loss that can be correlated with the decreasing of this Raman band. X-ray powder diffraction data suggest the moganite content in the samples to remain stable. We propose therefore the existence of a hitherto unknown Raman band at 503 cm−1 in chalcedony, assigned to ‘free’ Si–O vibrations of non-bridging Si–OH that oscillate with a higher natural frequency than bridging Si–O–Si (at 464 cm−1). A similar phenomenon was recently observed in the infrared spectra of chalcedony. The position of this Si–OH-related band is nearly the same as the Raman moganite band and the two bands may interfere. The actually observed Raman band in silica rocks might therefore be a convolution of a silanole and a moganite vibration. These findings have broad implications for future Raman spectroscopic studies of moganite, for the assessment of the quartz/moganite ratio, using this band, must take into account the contribution from silanole that are present in chalcedony and moganite.