Spectrally encoded microscopy uses a diffraction grating and a spectrum analysis setup to obtain microscopic images. The different positions on the sample are illuminated by different wavelengths. Then the spatial information is obtained by decoding the spectrum of reflection light. In this paper, a compact spectrally encoded microscopy (CSEM) is developed based on a swept source and a balanced detection. A fixed gain balanced detector is employed in the system to detect the weak sample light without amplifier. The lateral resolution of the system is measured by imaging a 1951USAF resolution test target. The imagings of excised swine small intestine and the finger skin in vivo are obtained to verify the imaging performance of biological tissue. The results show that the CSEM has the capability of generating depth-resolved imaging of biological tissue.