A measurement campaign was performed between 04/03/2013 and 17/07/2013 for simultaneous collection of PM2.5 samples in two nearby sites in southeastern Italy: an urban site and an urban background site. PM2.5 at the two sites were similar, however, the chemical composition and the contributions of the main sources were significantly different. The coefficients of divergence (CODs) showed spatial heterogeneity of EC (higher at the urban site because of traffic emissions) and of all metals. Major ions (NH4+, Na+, and SO42 −) and OC had low CODs suggesting a homogeneous distribution of sea spray, secondary sulphate and secondary organic matter (SOM = 1.6*OCsec, where OCsec is the secondary OC). The strong correlations between Na+ and Cl−, and the low Cl−/Na+ ratios, suggested the presence of aged sea spray with chloride depletion (about 79% of Cl−) and formation of sodium nitrate at both sites. In both sites, the non-sea-salt sulphate was about 97% of sulphate, and the strong correlation between SO42 − and NH4+ indicated that ammonium was present as ammonium sulphate. However, during advection of Saharan Dust, calcium sulphate was present rather than ammonium sulphate. The source apportionment was performed using the Positive Matrix Factorization comparing outputs of model EPA PMF 3.0 and 5.0 version. Six aerosol sources were identified at both sites: traffic, biomass burning, crustal-resuspended dust, secondary nitrate, marine aerosol, and secondary sulphate. The PMF3.0 model was not completely able, in these sites, to separate marine contribution from secondary nitrate and secondary sulphate from OC, underestimating the marine contribution and overestimating the secondary sulphate with respect to stoichiometric calculations. The application of specific constraints on PMF5.0 provided cleaner profiles, improving the comparison with stoichiometric calculations. The seasonal trends revealed larger biomass burning contributions during the cold period at both sites due to domestic heating emissions added to those of agricultural practices. Secondary aerosol represented about 50% of PM2.5 at both sites (about 1/3 due to SOM), with a slight increase during the cold season, probably due to the formation of secondary OC via gas-to-particle conversion. Secondary inorganic aerosol (nitrate plus sulphate) did not show seasonal trend because the reduction of nitrate due to thermal instability during the warm season was compensated by an almost equivalent increase of sulphate.