Magnetoacoustic tomography (MAT) is an emerging noninvasive electrical conductivity imaging that combines the high dielectric contrast of tissues and excellent resolutions of ultrasonography. In this paper, we have found the thermoacoustic (TA) effect in the measurement of MAT. Several materials with different conductivities have been measured by a MAT system with and without a static magnetic field. The acoustic signals have been analyzed and compared in the time domain and the frequency domain, respectively. It is found that the TA effect is related to the material characteristics. For the tissue-like materials with low conductivities, the TA signals caused by the TA effect are observable and cannot be ignored in the time and frequency domains. It means that the TA effect of biological tissues should be considered in MAT system in the future.