In the framework of bioanalytics and multiple array detection, we developed a fully portable and low-cost detection system based on Localized Surface Plasmon Resonance (LSPR) in a transmission configuration (T-LSPR). The transmission approach is suitable to be scaled to small dimension systems and to enable high-density array measurements on the same platform. Our setup is made out of off-the-shelf components and consists of a set of discrete light sources and a couple of light-detectors which enable a differential measurement setup. An algorithm fits the measured data and extracts the information of the plasmon peak position in the spectrum. The performance of our T-LSPR measurement system has been characterized on a set of Fluorinated Tin Oxide-coated glass slides covered with gold Nanoislands (NIs). The samples have been modified with a single-stranded DNA layer and a real-time DNA hybridization experiment has been performed. Here we demonstrate that the proposed T-LSPR device, based on the characterization of the plasmon peak with a differential approach, is able to monitor real-time DNA hybridization on surface, and to precisely measure the position of the peak with a standard deviation in wavelength of 0.2 nm.