The detection of explosives and their residues is of great importance in public health, antiterrorism and homeland security applications. The vapor pressures of most explosive compounds are extremely low and attenuation of the available vapor is often great due to diffusion in the environment, making direct vapor detection difficult. In this paper, a photonic-microfluidic integrated sensor for highly sensitive 2,4,6-Trinitrotoluene (TNT) detection is described based on an in-fiber Mach-Zehnder interferometer (MZI) in a photonic crystal fiber (PCF). A segment of PCF is inserted between standard single-mode fibers (SMF) via butt coupling to form a modal interferometer, in which the cladding modes are excited and interfere with the fundamental core mode. Due to butt coupling, the small air gap between SMF and PCF forms a coupling region and also serves as an inlet/outlet for the gas. The sensor is fabricated by immobilizing a chemo-recognition coating on the inner surface of the holey region of the PCF, which selectively and reversibly binds TNT molecules on the sensitized surface. The sensing mechanism is based on the determination of the TNT-induced wavelength shift of interference peaks due to the refractive index change of the holey-layer. The sensor device therefore is capable of field operation.