Bivalve mollusks can accumulate diarrheic shellfish poisoning (DSP) toxins through filter-feeding, but they exhibit some resistance to the toxins. Previous studies have suggested that the ABC transporters may have an important role in the resistance to DSP toxins, but comprehensive studies are lacking. In this study, we comprehensively analyzed the distribution of ABC transporters in the mussel Perna viridis, and observed responses of ABCB and ABCC transporters to the DSP toxins-producing dinoflagellate Prorocentrum lima. Total 39 members of ABC transporters were identified in P. viridis, including 3 full PvABCBs, 3 half PvABCBs, and 7 PvABCCs transporters. We found that PvABCBs and PvABCCs subfamilies were expressed in hemocytes, gills and digestive gland with some difference, especially in hemocytes. After exposure to P. lima, PvABCBs and PvABCCs displayed different expression changes in different tissues. The short-term (3 h) exposure to P. lima induced the transcription of PvABCB1_like1, PvABCB6, PvABCC1, PvABCC1_like and PvABCC1/3, and the longer-term (96 h) exposure increased the transcription of PvABCB1, PvABCB1_like, PvABCB10, PvABCC1 and PvABCC1_like1 in gills and PvABCC10 in digestive gland. These results suggest that different types of PvABCBs and PvABCCs in P. viridis may contribute to the detoxification of DSP toxins in different tissues at different time after exposure to DSP toxins. Our finding provides new evidence for further understanding the role of ABC transporters in the tolerance of mussel to DSP toxins.