We present the measurement of charge transport through phenylene conjugated molecules using electromigrated nanogap junctions. To elucidate the intrinsic transport properties of the conjugated molecular junctions, a variety of molecular transport techniques were performed at low temperature, including inelastic electron tunneling spectroscopy, temperature- and length-variable transport measurements, and transition voltage spectroscopy. Such a self-consistent characterization of the molecular junction demonstrates the observation of intrinsic molecular properties in these junctions.