We designed and implemented a hyperspectral microscope with structured illumination using the Olympus IX73 microscope as its basic platform. This system, which was designed and built in our Integrated Computational Optical Imaging Laboratory, combines two Digital Micromirror Devices (DMD) to compensate for the angular dispersion introduced by the blazed grating structure of the original DMD that was used to produce the structured illumination. Our hyperspectral microscope uses a supercontiuum laser illumination that can be spectrally filtered for desired wavelength ranges using an acoustic-optic filter. The system is controlled using LabVIEW, that allows for synchronous and asynchronous control of 1) illumination laser source, 2) acousto-optic filter, 3) spatial light modulator (DMD) and 4) camera. This LabView-based system control enables the implementation of a wide variety of image acquisition modes. Our microscope’s hyperspectral modality uses a wavelength-scanning configuration, where the supercontiuum laser illumination is filtered using an acousto-optic filter to produce very narrowband light for to acquire different hyperspectral images. Our system could be an excellent platform for implementing different types of hyperspectral data acquisition to implement, e.g., super-resolution microscopy and compressed sensing. The use of a DMD-based spatial light modulator allows for very fast spatial light modulation.