Electricity will become the main energy supplier to deliver energy services to the end consumer, being it residential, commercial or industrial. However, as part of the road to a fully carbon neutral energy system by 2050, molecules as energy carriers will play a key role. The paper describes the challenges for decarbonizing the different energy vectors and how choices are impacting energy efficiency. Two main routes exist to produce carbon-free hydrogen: classic approaches from carbon-based fuels equipped with Carbon Capture and Storage/incorporated in Carbon Capture and Use strategies, blue hydrogen or via electrolysis powered by renewable electric energy, green hydrogen. The direct use of hydrogen as a supplier of energy services to the end user is limited. Due to the specific characteristics of the hydrogen molecule (very light, very low boiling temperature, very low energy density), mobile applications are doubtful. For stationary applications, the need for storage of energy is clearly present, but the required volume and the resulting pressure/temperature needs make hydrogen a poor choice. The same holds for strategic energy storage. Hydrogen-based molecules, can be produced by combining CO2 captured from the air or industrial processes, making hydrogen an essential part of the carbon neutral post 2050 energy system, as an intermediate product. Molecules such as ammonia (NH3) may be used to transport hydrogen over long distances. The analysis leads to conclusions on the need for a clear taxonomy of hydrogen. The basis has to be the carbon content in order to ensure carbon neutrality in the most effective way.