This paper describes the results of a two-year monitoring study examining the pollution of the sea urchin Paracentrotus lividus by polycyclic aromatic hydrocarbons (PAHs) in Sardinia. GC-ITMS analysis of sea urchin gonads showed the presence of 11 and 12 PAHs in the samples of Capo Pecora, and Capitana, respectively. Fluorene, naphthalene and its two degradation products, 1-methyl-naphthalene, and 2-methyl-naphthalene, were detected in all samples analyzed. The ΣPAH residues showed a similar trend over the two-year sampling period. Furthermore, the residues in the first year were slightly higher than in the second year. The information obtained by the multivariate statistical analysis PLS-DA allowed for the determination of samples based on field site and varying habitat types (rocky reef, and Posidonia seabed). The results of this study showed that Posidonia sea urchins are contaminated by high molecular weight PAHs and that Capitana samples are more contaminated due to a higher level of human activity in the area.