Spatial and temporal distributions of isoprene and its oxidation products, methyl vinyl ketone and methacrolein in the Far East region of Russia were investigated. The measurement data were obtained from a mobile laboratory, which moved along the Trans-Siberian railway and from WRF-CHEM (Weather Research and Forecasting Chemical Model) and GEOS-CHEM (Goddard Earth Observing System Chemical Model) simulations. During the simulations, the RACM-MIM and MOZART mechanisms, included in the mesoscale WRF-CHEM model, as well as the Caltech Isoprene Scheme (CIS), built in the global GEOS-CHEM model, have been used. We found that the temporal distribution of the measured isoprene is in good agreement with the simulations. The measured isoprene, methyl vinyl ketone (MVK) and methacrolein (MACR) concentrations demonstrate pronounced diurnal variations. The correlation between the measured isoprene and MVK + MACR was good (R ~ 0.60–0.86). However, the simulated correlation between MVK + MACR and isoprene is very low, with the data for the night-time and daytime values varying. The simulated MVK + MACR to isoprene ratio, in comparison with the experimental result, has pronounced diurnal variations. During twilight and the night-time, the simulated MVK + MACR to isoprene ratio is more than 10. We propose that, due to the validity of the kinetic equations only in the homogeneous system, all chemical and transport (CTM) models, based on these kinetic equations, are not able to show an adequate simulation at night in the weak mixing atmosphere, when the atmospheric structure becomes heterogeneous. At moderate latitudes, we recommend the use of the turbulent Damköhler number and the Kolmogorov Damköhler numbers, which characterize the limits of CTM applicability, as the quality flags at the air quality forecast simulations.