This paper deals with the design of a Hybrid Energy Storage System (HESSs) for electric transportation such as Electric/Hybrid Vessel and Electric/Hybrid Train. The association of more than one Energy Storage Systems (ESSs) e.g., batteries which have different dynamics permit to take the advantages of the characteristics of both ESSs obtaining simultaneously a high energy density and high power density. This yields to a decrease in terms of the size of the main ESS and the total cost and an increase in terms of life span. The emulation of the batteries and with required control algorithm for the HESS are proposed. The design and the control of the HESSs is validated with the simulation in MATLAB/SIMULINK® environment and also with the real-time emulation of batteries in a laboratory setup of a HESS. The real-time experimental results have been validated against PC simulations showing full consistency. The setup of the hardware of HESS can be used to test any technologies of batteries, being a low cost solution for testing and benchmarking This work has been partially supported by the Spanish Government, Innovation Development and Research Office (MEC), under research grant ENE2013-44245-R, Project “Microholo”, and by the European Union through ERFD Structural Funds (FEDER). Also, this work has been partially supported by the government of Principality of Asturias, Foundation for the Promotion in Asturias of Applied Scientific Research and Technology (FICYT), under Severo Ochoa research grant, PA-13-PF-BP13138