This work examines and compares the performance of two emission datasets on modelling air quality concentrations for Spain: (i) the High-Elective Resolution Modelling Emissions System (HERMESv2.0) and (ii) the TNO-MACC-II emission inventory. For this purpose, the air quality system CALIOPE-AQFS (WRF-ARW/CMAQ/BSC-DREAM8b) was run over Spain for February and June 2009 using the two emission datasets (4 km x 4 km and 1 h). Nitrogen dioxide (NO2), sulphur dioxide (SO2), Ozone (O-3) and particular matter (PM10) modelled concentrations were compared with measurements at different type of air quality stations (i.e. rural background, urban, suburban industrial). A preliminary emission comparison showed significant discrepancies between the two datasets, highlighting an overestimation of industrial emissions in urban areas when using TNO-MACC-II. However, simulations showed similar performances of both emission datasets in terms of air quality. Modelled NO2 concentrations were similar between both datasets at the background stations, although TNO-MACC-II presented lower underestimations due to differences in industrial, other mobile sources and residential emissions. At Madrid urban stations NO2 was significantly underestimated in both cases despite the fact that HERMESv2.0 estimates traffic emissions using a more local information and detailed methodology. This NO2 underestimation problem was not found in Barcelona due to the influence of international shipping emissions located in the coastline. An inadequate characterization of some TNO-MACC-II's point sources led to high SO2 biases at industrial stations, especially in northwest Spain where large facilities are grouped. In general, surface O-3 was overestimated regardless of the emission dataset used, depicting the problematic of CMAQ on overestimating low ozone at night. On the other hand, modelled PM10 concentrations were less underestimated in urban areas when applying HERMESv2.0 due to the inclusion of road dust resuspension, whereas the underestimation at suburban industrial stations indicated deficiencies in fugitive emission sources characterization (agricultural operations, windblown dust emissions). (C) 2014 Elsevier Ltd. All rights reserved.