The Alexandrium tamarense species complex consists of 5 closely related species that are important bloom-forming dinoflagellates with a complex life cycle. The formation of resting cyst is a key strategy to resist harsh environmental conditions. In this study, the resting cysts of two major bloom-forming species of the A. tamarense species complex in China, A. catenella (Whedon & Kof.) Balech (previously A. fundyense, or A. tamarense species complex Group I) and A. pacificum Litaker (A. tamarense species complex Group IV), were studied in surface sediment collected from the Bohai Sea (BS) and Yellow Sea (YS) during two cruises conducted in 2012 and 2015. Cyst abundance of the A. tamarense species complex was first quantified by the primuline-staining method, and cysts of the two species were subsequently determined using two real-time quantitative PCR (qPCR) assays. Results showed that resting cysts of the A. tamarense species complex were more abundant in the YS than the BS (mean of 480 and 33 cysts g dry weight, DW⁻¹ of sediment, respectively). Cysts were mainly found in the central portion of the northern YS, the area SE (southeast) of the Shandong peninsula, and the area near the Subei Shoal in the southern YS, where surface sediment had a high percentage of clay and silt (particle size < 63 μm) content. The maximum cyst abundance recorded was 3090 cysts g DW⁻¹ of sediment in 2012 and 3448 cysts g DW⁻¹ in 2015, respectively. Cysts were mainly composed of A. catenella in the YS and the BS, while those of A. pacificum were only detected occasionally at some sampling sites in the YS. Highly abundant resting cysts in surface sediment of the YS may serve as “seed banks” for recurrent toxic blooms of A. catenella and the associated shellfish contamination by paralytic shellfish toxins in the YS.