Knowledge about isoprene emissions and concentration distribution is important for chemistry transport models (CTMs), because isoprene acts as a precursor for tropospheric ozone and subsequently affects the atmospheric concentrations of many other atmospheric compounds. Isoprene has a short lifetime, and hence it is very difficult to evaluate its emission estimates against measurements. For this reason, we coupled two isoprene emission models with the Danish Eulerian Hemispheric Model (DEHM), and evaluated the simulated background ozone concentrations based on different models for isoprene emissions. In this research, results of using the two global biogenic emission models; GEIA (Global Emissions Inventory Activity) and MEGAN (the global Model of Emissions of Gases and Aerosols from Nature) are compared and evaluated. The total annual emissions of isoprene for the year 2006 estimated by using MEGAN is 592 T -1 for an extended area of the Northern Hemisphere, which is 21% higher than that estimated by using GEIA. The overall feature of the emissions from the two models is quite similar, but differences are found mainly in Africa's savannah and in the southern part of North America. Differences in spatial distribution of emission factors are found to be a key source of these discrepancies. In spite of the short life-time of isoprene, a direct evaluation of isoprene concentrations using the two biogenic emission models in DEHM has been made against available measurements in Europe. Results show an agreement between two models simulations and the measurements in general and that the CTM is able to simulate isoprene concentrations. Additionally, investigation of ozone concentrations resulting from the two biogenic emission models show that isoprene simulated by MEGAN strongly affects the ozone production in the African savannah; the effect is up to 10% more than that obtained using GEIA. In contrast, the impact of using GEIA is higher in the Amazon region with more than 8% higher ozone concentrations compared to that of using MEGAN. Comparing the ozone concentrations obtained by DEHM using the two different isoprene models with measurements from Europe and North America, show an agreement on the hourly, mean daily and daily maximum values. However, the average of ozone daily maximum value simulated by using MEGAN is slightly closer to the measured value for the average of all measuring sites in Europe. © 2012 Author(s).