Three-dimensional large eddy simulations (LES) of highly underexpanded hydrogen and nitrogen jets at the same nozzle pressure ratio (NPR) of 5.60 and at a Reynolds number around 105 are performed. The classical near-field structures of highly underexpanded jets are well captured by LES, especially the shape and size of Mach barrel for both jets are very similar and agree well with the available literature data. However, the flow field and the shock structures after the Mach disk differ significantly. The density in the annular shear layer of H-2 jet is much lower because of its smaller molecular weight. Meanwhile, the H-2 jet has a much longer jet core and more shock cells. The dominant instability mode is helical for the N-2 jet, but is axisymmetric for the H-2 jet. There are two discrete peaks of f(s) = 37.086 kHz and f(2s) = 45.695 kHz in the spectrum of the N-2 jet, while the spectrum of the H-2 jet is characterized by a fundamental screech frequency of f(s) = 47.020 kHz and its high-order harmonics. The H-2 jet mixes more rapidly with the ambient air but has a much smaller mixing area on cross-section planes. Mixing between the ambient air and fuel still takes places at the jet boundary defined according to the mixture fraction of Z = 0.02, and the area of fully turbulent region of the highly underexpanded jets seems to be less predicted based on the traditional vorticity T/NT (turbulent/non-turbulent) interface for both jets. Copyright (C) 2016, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.