Two-photon microscopy (TPM) has been used in plant research as a high-resolution high-depth 3D imaging modality. However, TPM is known to induce photo-damage to the plant in case of long time exposure, and optimal excitation wavelength for plant imaging has not been investigated. Longer excitation wavelength may be appropriate for in vivo two-photon imaging of Arabidopsis thaliana leaves, and effects of longer excitation wavelength were investigated in terms of imaging depth, emission spectrum. Changes of emission spectrum as a function of exposure time at longer excitation wavelength were measured for in vivo longitudinal imaging. Imaging depth was not changed much probably because photon scattering at the cell wall was a limiting factor. Chloroplast emission spectrum showed its intensity peak shift by 20 nm with transition of excitation wavelength from 849 nm or below to 850 nm or higher. Emission spectrum showed different change patterns with excitation wavelengths in longitudinal imaging. Longer excitation wavelengths appeared to interact with chloroplasts differently in comparison with 780 nm excitation wavelength, and may be good for in vivo imaging.