The aim of the paper was the identification of frequency synchronization phenomenon occurring between different groups of e-learning system users. The changes in time of daily logs of: administration workers, teachers and students have been analyzed. The following analyses: correlation, Fourier and wavelet have been used to identify the nature of data. Basing on the wavelet analysis it has been proposed the new criterion of evaluation of frequency synchronization of two chaotic systems. The modified wavelet power spectrum has been used to identify the frequency synchronization between chaotic behaviors of three groups of users of e-learning web system. Obtained results have shown that the proposed method is useful for analyzing the phenomena of frequency synchronization of user groups of e-learning system.