In this study, a lens-free dual-color bio-imaging system is developed. This system utilizes a small CMOS image sensor chip as the imager. By coupling alternate lines of blue and yellow-green filters coated on photodiodes, we can simultaneously detect cyan and yellow fluorescent lights using the device. By equipping the device with a hybrid filter made of a bandpass interference filter, a fiber optic plate (FOP), and a pale-yellow absorption filter, we can achieve an excitation light extinction ratio of approximately −57 dB. By using fluorescent beads of two different colors, we can confirm the operation of the image sensor. Individual images from the cyan and yellow channels can be obtained after data processing, and subsequently the yellow-to-cyan image ratio can also be determined. The results show that our device can be used to study Förster resonance energy transfer (FRET) and can thus be applied to investigate the progression of diseases such as cancer.