A self-started, switchable dual-wavelength all-polarization-maintaining mode-locked (ML) fiber laser for optical parametric generation (OPG) in photonic crystal fiber (PCF) applied to coherent anti-stokes Raman scattering (CARS) microscopy is reported in this paper. The complete laser setup is built in an all-fiber structure composed of commercial elements. It is based on a linear cavity with an active medium—namely, Ytterbium-doped fiber (YDF), a pair of fiber Bragg gratings as switchable partial mirrors between 1031.5 and 1049.7 nm, and a semiconductor saturable absorber mirror functioning also as the mode-locking device. The seed laser is amplified to 650 mW average power by two YDF amplifiers. The source delivers a pulse-train output of 30.9 ps at 1031.5 ps and 31.6 ps at 1049.7, a 3.1-MHz repetition rate, and over 200 nJ pulse energy and 6 kW of peak power at fundamental ML operation. The properties of this switchable dual-wavelength source ensures the correct OPG by degenerated four-wave mixing in PCF fulfilling the phase matching condition which corresponds to CARS resonance of 2850 $ {\mathbf{c}}{ {\mathbf{m}}^{ - 1}}$ (CH3-O molecular bonds) at 1031.5 nm and 1475 $ {\mathbf{c}}{ {\mathbf{m}}^{ - 1}}$ (CH2 δ molecular bonds) at 1049.7 nm.