Molybdenum oxides exhibit quite interesting structural, chemical, electrical, optical and electrochemical properties. These materiails are promising in numerous current and emerging technological applications, which include nano-electronics, optoelectronics, energy storage and micromechanics. However, fundamental understanding of the crystal structure and engineering the phase and microstructure is the key to achieving the desired properties and performance in all of these applications.  Furthermore, the properties and phenoena of these oxides dependent on the synthetic procedures and fabrication conditions. In this context, we present some illustrative examples to highlight the fundamental scientific issues, challenges, and opportunities as related to various Mo-oxides applicable to electrochemical energy applications. Specific attention is given to batteries, while other energy related applications are also considered. Due to the wide range of oxidation states (from +6 to +2) they are promising as both positive (cathode) and negative (anode) electrodes of electrochemical cells. Based on the results and analyses, the approaches adopted for enhanced performance and/or improvements will be discussed.