In this work, we report a performance comparison of an acousto-optic tunable filter (AOTF), and a liquid crystal tunable filter (LCTF) based on a novel dual-arm hyperspectral imaging (HSI) configuration. The main purpose of this work is to highlight the leverage points of each tunable filter, in order to facilitate filter choice in HSI design. Three main parameters are experimentally examined: spectral resolution, out-of-band suppression, and image quality in the sense of spatial resolution. The experimental results, using wideband illumination, laser lines, and a spatial test target (USAF-1951) emphasized the superiority of AOTF in spectral resolution, out-of –band suppression and random switching speed between wavelengths. The same experiments demonstrated LCTF to have better performance in terms of the spatial image resolution, both horizontal and vertical, and high definition quality. In conclusion, the efficient design of an HSI system is application-dependent. For medical applications, for instance, if the tissue of interest has undefined optical properties, or contains close spectral features, AOTF might be the better option. Otherwise, LCTF is more convenient and simpler to use, especially if the tissue chromophore’s spatial mapping is needed.