The combination of two-photon microscopy (TPM) and optical coherence tomography (OCT) is useful in conducting in-vivo tissue studies, because they provide complementary information regarding tissues. In the present study, we developed a new combined system using separate light sources and scanners for individually optimal imaging conditions. TPM used a Ti-Sapphire laser and provided molecular and cellular information in microscopic tissue regions. Meanwhile, OCT used a wavelength-swept source centered at 1300 nm and provided structural information in larger tissue regions than TPM. The system was designed to do simultaneous imaging by combining light from both sources. TPM and OCT had the field of view values of 300 μm and 800 μm on one side respectively with a 20x objective. TPM had resolutions of 0.47 μm and 2.5 μm in the lateral and axial directions respectively, and an imaging speed of 40 frames/s. OCT had resolutions of 5 μm and 8 μm in lateral and axial directions respectively, a sensitivity of 97dB, and an imaging speed of 0.8 volumes per second. This combined system was tested with simple microsphere specimens, and was then applied to image small intestine and ear tissues of mouse models ex-vivo. Molecular, cellular, and structural information of the tissues were visualized using the proposed combined system.