To improve the ability of an external cavity laser (ECL) biosensor to more easily distinguish true signals caused by biomolecular binding from a variety of sources of background noise, two photonic crystal (PC) resonant reflectors were incorporated into a single flow cell, with one of the PCs performing the detection function and the other one serving as a reference sensor. The ECL-based sensor system simultaneously emits at two distinct wavelengths corresponding to two different longitudinal cavity modes selected by the sensing and reference PC reflectors. The surface of the sensing PC filter was functionalized by a biomolecule recognition layer and exhibited narrowband reflection with the peak reflection wavelength at 856 nm. The reference PC was untreated and had the peak reflection wavelength at 859 nm. The PCs were bond to the upper and lower surfaces of a thin chamber frame, forming a flow cell. Utilizing the reference external cavity mode, the dual-mode ECL sensor system eliminated common-mode noise sources, including thermal drift, refractive index variations of the analyte solution, and nonspecific biomolecule binding.