To achieve optical biopsy for gastro-intestinal (GI) endosopy with the use of nonlinear optical (NLO) endomicroscopes, integration of NLO technology with the design of a conventional flexible GI endoscope is necessary. One key challenge has been to design an NLO distal tip which can be compatible with flexible GI endoscopy retroflexion curvature radius as small as 20 mm to provide bending angle up to 210 degrees; the state-of-the-art NLO miniaturized design still consists of a long rigid “needle” shape probe at the distal end that can be damaged during the retroflex procedure when passing through the instrument channel of a flexible GI endoscope for in vivo imaging. To circumvent this design challenge, authors present a line scan multiphoton endomicroscope utilizing a novel simplified microelectromechanical systems (MEMS) scanner. This unique MEMS scanner consists of a customized single-axis dichroic MEMS scanner (SADMS) and vibrates at the back focal point of a customized micro-objective lens. This work demonstrates the new NLO scanner design can be compatible with conventional flexible GI endoscope to offer in situ functional microscopic imaging capability.