Τhis study aims to measure the abundance of microplastic (MP) particles in the soft tissue of mussel (Mytilus galloprovincialis) and pearl oyster (Pinctada imbricata radiata) specimens. Samples were collected at four sites in Greece (Sagiada, Malesina, Elounda, Rhodes) from wild and farmed populations. The identification of MPs was accomplished by Raman spectroscopy. Comparisons were made between the two different species where the two species co-existed (Malesina), between the four study sites (five sampling stations) in relation to P. imbricata radiata individuals, and also in every station for the different MP types found. For the specimens from Malesina, M. galloprovincialis had more MPs in their soft tissue compared to P. imbricata radiata. Microfibers were found in abundance in M. galloprovincialis, while microfragments were found in P. imbricata radiata specimens. The main MP type found in P. imbricata radiata specimens was microfragments in all five sampling stations, and ranged between 1.54 ± 0.63 (Rhodes-baskets) and 3.56 ± 0.35 (Sagiada) MP particles/g. While the samples of mussels and pearl oysters were similar in age, the differences found in the concentrations of MPs appears to be due to their different farming methods and location characteristics concerning the five sampling stations of pearl oysters. This study indicates that the culturing system does not affect MP concentration in bivalves, and further investigation is needed to find the most appropriate method to limit and reduce MPs that end up in the farmed organisms.