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Aerosols generated by incomplete combustion of fossil fuels (FF) are major air pollutants. Aerosol emissions of transport systems are currently acknowledged to be a largest source of uncertainties in understanding the impacts on regional air quality. Ship emission is among the world’s highest polluting sources per quality of fuel consumed. Combustion aerosols may serve tracers allowing a link to distinct combustion sources in apportionment studies if their key physico-chemical characteristics representative the emission sources are defined. The estimations of the source contribution to ambient particulates assume specific markers different from other combustion sources. A complexity of multicomponent and source-specific PM emissions requires the characterization of individual particles (Bladt et al., 2012). Presently, hierarchical cluster analysis (HCA) is a data analysis technique which is used for interpretation of electron microprobe analysis data and determination of particle types in ambient air with a large number of pollution sources. Here, we present the development of HCA for characterization of FF emissions by classification of individual particle data on characteristic groups with similar morphological and chemical composition according to source and fuel used. Scanning electron microscopy (SEM) coupled with energy-dispersive X-ray spectroscopy (EDX) is used for characterization of morphology and composition of a large number of individual particles. Clustering expert analysis assures the mean composition of groups closed to physico-chemical identifiable types of particles. This approach allows quantifying the various diesel and biomass burning sources and identifying the specific characteristic features that can serve as micromarkers of emission source (Popovicheva et al, 2012). This paper reviews the quantification of particulate combustion emission microstructure and identification of characteristic morphological and chemical micromarkers of source-specific combustion aerosols emitted by transport systems (road and marine diesel engines) and wildfires. Impact of Fe content on microstructure of soot particles was analysed in Bladt et al. (2012) to demonstrate the elaborated approach for separation of individual particles into characteristic groups representing the particle types in dependence on iron content. Microscopic and chemical characterization of Opel Astra diesel engine exhaust operated at 35 km/h speed and used diesel B0 fuel with various lube oil (low and high SAPS) and biodiesel fuel B20 with high SAPS are performed (Popovicheva et al., 2014). The most abundant group (around 50%) in each exhaust is Soot containing chain agglomerates of primary particles of C and O mostly. In diesel B0 exhaust particles, low SAPS, groups of silicates, iron, and aluminum oxides are also found. Using high SAPS with larger ash content leads to abundance of groups of Al oxide and Al fused with Fe. The most prominent impact of high SAPS using relates with the presence of well-separated groups of Nb oxides and W particles served as micromirkers of lube oil. Biodiesel exhaust particles, high SAPS, contain the groups of Fe and Zn oxides, and W particles. The source specific micromarker of biodiesel particles is a separate group enriched by Cl, K, and Na, the elements which are commonly recognized as biomarkers of biofuel combustion. Exhausts from the main and auxiliary engines operated onboard of a RoRo/casetter carrier ship during TRANSFORM campaign, burning heavy and distillate fuels, respectively, are analyzed (Popovicheva et al., 2012). SEM/EDX observations of emitted aerosols indicate carbonaceous particles internally and externally mixed with inorganic species in the combination of spherical and irregular shapes. The composition of individual particles is varying in a wide concentration range of major elements (C, O) and impurities (S, Fe, Si, Ca, Zn, V, Ni, K, Mn) representative the origin of fuels. In distillate fuel (DF)-derived aerosols we identify groups Soot, Ca- and Fe/Si-rich particles. Calcium sulfate/oxide/carbonates and iron oxides are found to compose the group of Ca- and Fe-rich particles, respectively, while silicon oxide and silicate determine the group of Si-rich particles in heavy fuel (HF)-derived emission. Transition metals (V, Ni) containing particles specify the separate group which may serve as a specific micromarker of heavy fuel combustion. State-of-the-art characterization of complex multicomponent aerosols improves the quantification of contribution of various fossil fuel emissions to ambient particulates and the identification of a source type in the apportionment studies. This work was supported by RFBR projects 12-05-00395_а and 12-05-92002. Bladt, H., Schmid, J., Kireeva, E., Popovicheva, O.B. et al. (2012). Aerosol Science and Technology, 46, 1337-1348. Popovicheva O., Kireeva E., Shonija. N. et al. (2012). J. Environ. Monit., 14, 3101 – 3110. Popovicheva O., Kireeva E., Steiner S., B. Rothen et al, AAQR, accepted.