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Despite the increase of commercial shipping around the world, data are yet relatively scarce on the contribution of these emissions to ambient air particulates. One of the reasons is the complexity in the detection and estimation of shipping contributions to ambient particulates in harbor and urban environments, given the similarity with tracers of other combustion sources. This study aimed to identify specific tracers of shipping emissions in a Mediterranean city with an important harbor (Melilla, Spain). Results showed that, for 24 h PM10 and PM2.5 samples, valid tracers of commercial shipping emissions were ratios of V/Ni = 4−5 and V/EC < 2, whereas V/EC > 8 excluded the influence of shipping emissions. Other ratios (V/S, La/Ce, Zn/Ni, Pb/Zn, OC/EC) and tracers (Pb, Zn) were also tested but did not correlate with this source. Due to the changing composition of diesel fuels, tracers in the Mediterranean Sea may not be representative in other regions of the world and vice versa. The contribution of shipping emissions to ambient particulate matter (PM) urban background levels was quantified by positive matrix factorization (PMF), resulting in 2% and 4% of mean annual PM10 levels (0.8 μg/m3 primary particles and 1.7 μg/m3 secondary particles, with 20% uncertainty) and 14% of mean annual PM2.5 levels (2.6 μg/m3).