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One way to resolve the paralytic shellfish poisoning problem is to reduce the number of causative plankton cysts through dredging. However, due to the long-term survival capabilities of Alexandrium cysts, suppressing germination remains a challenge, particularly in areas where these cysts are buried deep within sediments. This challenge could be mitigated by utilizing macrobenthic organisms, specifically deposit feeders, which are capable of ingesting ellipsoidal Alexandrium cysts. In this study, we examined whether three macrobenthic organisms collected from Ofunato Bay, along the Pacific coast of northern Japan, influence the abundance and germination of ellipsoidal Alexandrium cysts through ingestion experiments. The cyst counts in the sediments from ingestion experiments with Thyasira tokunagai (Mollusca) and Maldanidae sp. (Annelida) remained unchanged compared to the control, whereas a significant reduction was observed in the sediments from ingestion experiments with Theora lata (Mollusca). The digestion rate of ellipsoidal Alexandrium cysts by T. lata amounted to 375 cysts per individual per day. Moreover, the germination percentage in the presence of all three macrobenthic organisms declined compared to the control. These findings suggest that T. lata, which are highly concentrated in Ofunato Bay, are effective at removing ellipsoidal Alexandrium cysts and suppressing their germination.