The CRIRES instrument on the Very Large Telescope was used to make high-resolution (R=100,000) observations of Jupiter in the 4.5-5.2 μm spectral range. At these wavelengths, Jupiter’s atmosphere is optically thin and the spectra are sensitive to the 4-8 bar region. The primary use of this dataset is therefore to study the abundances of minor molecular species in Jupiter’s troposphere, including CH3D, GeH4, AsH3 and PH3. However we also used these observations to identify sixteen previously undetected H3+ emission lines from Jupiter’s ionosphere. These emission lines are so strong that they are visible even against the bright background radiation from the troposphere. We measured the Doppler broadening of the H3+ emission lines in order to evaluate the kinetic temperature of the molecules, and we obtained a value of 1390±160 K. We also measured the relative intensities of lines in the ν2 fundamental in order to calculate the rotational temperature, obtaining a value of 960±40 K. Finally, we used the detection of an emission line from the 2ν2(2)-ν2 overtone to measure a vibrational temperature of 925±25 K. We use these three independent temperature estimates to discuss the thermodynamic equilibrium of Jupiter's ionosphere.