Atmospheric chemistry and transport of mercury play a key role in the global mercury cycle. However, there are still considerable knowledge gaps concerning the fate of mercury in the atmosphere. This is the second part of a model inter-comparison study investigating the impact of atmospheric chemistry and emissions on mercury in the atmosphere. While the first study focused on ground based observations of mercury concentration and deposition, here we investigate the vertical distribution and speciation of mercury from the planetary boundary layer to the lower stratosphere. So far, there have been few model studies investigating the vertical distribution of mercury, mostly focusing on single aircraft campaigns. Here, we present a first comprehensive analysis based on various aircraft observations in Europe, North America, and on inter-continental flights. The investigated models proved to be able to reproduce the distribution of total and elemental mercury concentrations in the troposphere including inter-hemispheric trends. One key aspect of the study is the investigation of mercury oxidation in the troposphere. We found that different chemistry schemes were better at reproducing observed oxidized mercury (RM) patterns depending on altitude. High RM concentrations in the upper troposphere could be reproduced with oxidation by bromine while elevated concentrations in the lower troposphere were better reproduced by OH and ozone chemistry. However, the results were not always conclusive as the physical and chemical parametrizations in the chemistry transport models also proved to have a substantial impact on model results.