Digital difference filters were used for the analysis of data of the spectral observations of the rotational temperature and emission intensity of vibrationally excited hydroxyl (OH*) at altitudes 85–90 km at observatories Zvenigorod (56° N, 37° E) for 2004–2016 years and Tory (52° N, 103° E) for 2012–2017. The monthly-average values and standard deviations of mesoscale perturbations of the OH* emission characteristics with periods 0.8–11 h are obtained. These mesoscale perturbations may reflect internal gravity waves (IGWs) in the mesopause region. To filter out mesoscale perturbations, differences between the sequential values of the OH* emission characteristics, averaged over the intervals by duration from 0.5 h to 2 h, were obtained. The average monthly variances of mesoscale perturbations in the OH* rotational temperature obtained at Tory are larger compared to Zvenigorod ones. Average seasonal changes of relative mesoscale variances demonstrate maxima in winter and in summer, with the summer maximum shifted closer to spring months for the Tory station. The reasons for the differences could be different orography and jet streams in the lower and middle atmosphere, also different spectra of IGW horizontal wavelengths due to different geometry of observations at Tory and Zvenigorod.