Pyrodinium bahamense has been one of the most frequently blooming dinoflagellate species in the years 2016–2018 in Cirebon waters, Indonesia, and is also related to several cases of paralytic shellfish poisoning (PSP). This study aimed to examine the distribution of the cysts of P. bahamense in the sediments of Cirebon waters. The cyst density of P. bahamense in the study area ranged from 27 to 493 cysts/g of wet sediment. The highest abundance of P. bahamense cysts was recorded in sampling sites with high anthropogenic activities, coinciding with the sites having a higher percentage of silt and clay in the sediment and where periodic dinoflagellates blooms occur. These results indicate the need for further studies to understand the dynamics of P. bahamense population in Cirebon and mitigate its future bloom. Measurement of factors such as pollution, eutrophication, water circulation, and sediment transport will have to be done.