In this paper, we propose a holographic scanning based confocal microscope that works in both the reflection and fluorescence modes. Here, the illumination beam is scanned using a reconfigurable binary hologram instead of a usual galvanometer mirror scanner. The reconfigurable hologram is implemented using a liquid crystal spatial light modulator. Two different lasers are used for fluorescence and reflection mode imaging with the phase profile of the illumination beam, derived from each laser, described by the holograms. We demonstrate the working of our microscope in both the modes by imaging a section of tooth specimen stained with a fluorescent dye.