Fine particle samples were collected during summer at an urban (LIM) and a rural/background (AGM) site of Cyprus. They were analyzed for pinene and isoprene secondary organic aerosol (PSOA-ISOA) tracers, linear dicarboxylic acids (DCAs), hydroxyacids (HAs), aromatic acids (AAs), monocarboxylic acids (MCAs) and levoglucosan by GC/MS with prior 3-step derivatization. DCAs, AAs, MCAs and levoglucosan exhibited significantly higher concentrations (p < 0.05) in LIM, PSOAs and ISOAs in AGM (p < 0.05), whereas mixed trends were found for HAs. Among DCAs, succinic was the most abundant in both sites, accounting for 42.5% and 36.5% of the total DCAs in LIM and AGM respectively, followed by adipic in LIM (20.1%) and azelaic in AGM (22.4%). Malic, phthalic and palmitic acids were the dominant HA, AA and MCA, respectively. Regarding PSOAs, significant differences were observed between the two sites, with the first-generation products accounting for 59.8% of the total measured PSOAs in AGM, but were remarkably lowered (10.3%) in LIM indicating that they were highly oxidized. 2-Methylerythritol was the dominant ISOA tracer in both sites; nevertheless the elevated relative abundance of 2-methylglyceric acid in LIM implies the influences of higher NOx levels. The increased O3 levels observed in AGM appear to have a significant impact on SOA formation. Source apportionment tools employed revealed factors related to secondary formation processes including oxidation of unsaturated fatty acids, pinene, isoprene and anthropogenic VOCs and factors associated with primary sources such as biomass burning, plant emissions and/or cooking and motor exhaust, with noteworthy differences observed between the two areas.