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Air pollution is one of the main environmental concerns in urban areas, where anthropogenic emissions strongly affect air quality. This work presents the first spatially resolved detailed characterization of PM2.5 (particulate matter with aerodynamic equivalent diameter daero ≤ 2.5 µm) in two major Estonian cities, Tallinn and Tartu. The measurements were performed in March 2014 using a mobile platform. In both cities, the non-refractory (NR)-PM2.5 was characterized by a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) using a recently developed lens which increases the transmission of super-micron particles. Equivalent black carbon (eBC) and several trace gases including carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were also measured. The chemical composition of PM2.5 was found to be very similar in the two cities. Organic aerosol (OA) constituted the largest fraction, explaining on average about 52 to 60 % of the PM2.5 mass. Four sources of OA were identified using positive matrix factorization (PMF): hydrocarbon-like OA (HOA, from traffic emissions), biomass burning OA (BBOA, from biomass combustion), residential influenced OA (RIOA, probably mostly from cooking processes with possible contributions from waste and coal burning), and oxygenated OA (OOA, related to secondary aerosol formation). OOA was the major OA source during nighttime, explaining on average half of the OA mass, while during daytime mobile measurements the OA was affected by point sources and dominated by the primary fraction. A strong increase in the secondary organic and inorganic components was observed during periods with transport of air masses from northern Germany, while the primary local emissions accumulated during periods with temperature inversions. Mobile measurements offered the identification of different source regions within the urban areas and the assessment of the extent to which pollutants concentrations exceeded regional background levels (urban increments). HOA, eBC, CO2, and CO showed stronger enhancements on busy roads during the morning and evening traffic rush hours; BBOA had its maximum enhancement in the residential areas during the evening hours and RIOA was enhanced in both the city center (emissions from restaurants) and in the residential areas (emissions from residential cooking). In contrast, secondary components (OOA, sulfate (SO4), nitrate (NO3), ammonium (NH4), and chloride (Cl)) had very homogeneous distributions in time and space. We were able to determine a total PM2.5 urban increment in Tartu of 6.0 µg m−3 over a regional background concentration of 4.0 µg m−3 (i.e., a factor of 2.5 increase). Traffic exhaust emissions were identified as the most important source of this increase, with eBC and HOA explaining on average 53.3 and 20.5 % of the total increment, respectively.