A comprehensive aerosol characterization was conducted at Marseille during summer, including organic (OC) and elemental carbon (EC), major ionic species, radiocarbon (14C), water-soluble OC and HULIS (HUmic LIke Substances), elemental composition and primary and secondary organic markers. This paper is the second paper of a two-part series that uses this dataset to investigate the sources of Organic Aerosol (OA). While the first paper investigates the primary sources (El Haddad et al., 2010), this second paper focuses on the secondary fraction of the organic aerosol. In the context of overall OC mass balance, primary OC (POC) contributes on average for only 22% and was dominated by vehicular emissions accounting on average for 17% of OC. As a result, 78% of OC mass cannot be attributed to the major primary sources and remains un-apportioned. Radiocarbon measurements suggest that more than 70% of this fraction is of non-fossil origin, assigned predominantly to biogenic secondary organic carbon (BSOC). Therefore, contributions from three traditional BSOC precursors, isoprene, $\alpha $-pinene and β-caryophyllene, were considered. These were estimated using the ambient concentrations of Secondary Organic Aerosol (SOA) markers from each precursor and laboratory-derived marker mass fraction factors. Secondary organic markers derived from isoprene photo-oxidation (ie: 2-methylglyceric acid and 2-methyltetrols) do not exhibit the same temporal trends. This variability was assigned to the influence of NOx concentration on their formation pathways and to their potential decay by further processing in the atmosphere. The influence of changes in isoprene chemistry on assessment of isoprene SOC contribution was evaluated explicitly. The results suggest a 60-fold variation between the different estimates computed using different isoprene SOC markers, implying that the available profiles do not reflect the actual isoprene SOC composition observed in Marseille. Using the marker-based approach, the aggregate contribution from traditional BSOC was estimated at only 4.2% of total OC and was dominated by α-pinene SOC accounting on average for 3.4% of OC. As a result, these estimates underpredict the inexplicably high loadings of OC. This underestimation can be associated with (1) uncertainties underlying the marker-based approach, (2) presence of other SOC precursors and (3) further processing of fresh SOC, as indicated by organosulfates (RSO4H) and HUmic LIke Substances (HULIS) measurements.