The toxic dinoflagellate Karenia mikimotoi frequently forms harmful algal blooms (HABs) and thus causes massive kills of fish and shellfish in worldwide coastal waters, which has led to intensive investigations on multiple facets of the species. Following our recent discovery of K. mikimotoi forming resting cyst, a very possible mechanism for the inoculation of blooms and geographic expansion for this and many other HABs-causing species, here we report our detection of K. mikimotoi resting cysts in 125 surface sediment samples collected from the coastal waters (covering a latitude range from 18.29 N to 39.85 N and 3 sediment cores (accumulated in 70-100 years) collected from the East China Sea where are adjacent to the frequent blooming areas of K. mikimotoi. Via applications of quantitative real-time PCR (LSU rDNA-targeted), species-specific fluorescence in situ hybridization (FISH), and nested-PCR-and-sequencing to both types of the sediment samples that were pretreated with sodium polytungstate solution (SPT), we demonstrated that 1) K. mikimotoi cysts are widely present in surface sediments of the China seas (Bohai Sea (BS), Yellow Sea (YS), East China Sea (ECS), and South China Sea (SCS)), 2) the abundance of cysts is generally low (0 to 33 cysts in 32 g wet sediment), with that in the ECS and the SCS being higher than that in the YS and the BS, and the highest abundance was observed in sites of the ECS (e.g., Ningde, Fujian province) where the blooms of the species occurred frequently, as quantified by both methods, and 3) the cysts of K. mikimotoi have been present in the sediments of the ECS since 1970s, a short time prior to the first recorded bloom of K. mikimotoi in the SCS at 1980s. Our results not only demonstrated the wide geographic distribution of resting cyst of K. mikimotoi along the coast of China, but also proved a 50 years preservation of the cysts in the sediments of coastal area prone to forming frequent blooms. We consider our results have provided critical insights into the mechanisms of frequent bloom outbreaks and global distribution of K. mikimotoi in general, and particularly into the historical origin of K. mikimotoi in China. Further investigations are suggested to focus on on-site surveys for the cyst production and germination rates.