Benzo(a)pyrene (B(a)P) is a well-known genotoxic agent, the removal of which from environmental matrices is mandatory, necessitating the application of cleaning strategies that are harmless to human and environmental health. The potential application of nanoparticles (NPs) in the remediation of polluted environments is of increasing interest. Here, specifically designed NPs were selected as being non-genotoxic and able to interact with B(a)P, in order to address the genetic and chromosomal damage it produces. A newly formulated pure anatase nano-titanium (nano-TiO2), a commercial mixture of rutile and anatase, and carbon black-derived hydrophilic NPs (HNP) were applied. Once it had been ascertained that the NPs selected for the work did not induce genotoxicity, marine mussel gill biopsies were exposed in vitro to B(a)P (2 μg/mL), alone and in combination with the selected NPs (50 µg/mL nano-TiO2, 10 µg/mL HNP). DNA primary reversible damage was evaluated by means of the Comet assay. Chromosomal persistent damage was assessed on the basis of micronuclei frequency and nuclear abnormalities by means of the Micronucleus-Cytome assay. Transmission Electron Microscopy (TEM) was performed to investigate the mechanism of action exerted by NPs. Pure Anatase n-TiO2 was found to be the most suitable for our purpose, as it is cyto- and genotoxicity free and able to reduce the genetic and chromosomal damage associated with exposure to B(a)P.