Vibrational and rotational excitation of the hydrogen molecule can significantly effect molecular reaction rates in low pressure low temperature plasmas, for example for the creation of H − /D − ions via the dissociative attachment process. In general, the rotational population in these discharges is known to be non-thermal with an overpopulation of states with high rotational quantum number N. In contrast to a sophisticated direct measurement of the rotational distribution in the X 1 Σ + g , v = 0 state, it is demonstrated that the determination can also be carried out up to high-N levels rather easily via optical emission spectroscopy utilizing the Fulcher-α transition of H 2 and D 2. The measured rotational populations can be described with a two-temperature distribution where the cold part reflects the population according to the gas temperature of the discharge. This has been verified by using the emission of the second positive system of nitrogen as independent gas temperature diagnostic. The hot part where the rotational temperature reaches several thousand Kelvin arises most probably from recombinative desorption of hydrogen at the discharge vessel wall where parts of the binding energy are converted into rotational excitation. Neglecting the hot population-what is often done when using the Fulcher-α transition as gas temperature diagnostic-can lead to a strong overestimation of T gas. No fundamental differences in the rotational distributions between hydrogen and deuterium have been found, only the hot rotational temperature is smaller for D 2 indicating an isotope-dependency of the recombinative desorption process.