A new organic-walled dinoflagellate cyst species, Spiniferites multisphaerus sp. nov., is described from Late Quaternary sediments of Guaymas Basin, Gulf of California (Mexico). This species is characterized by a pronounced apical protuberance and bubble-like elements that comprise the central body wall, sutural septae and processes. The central body wall is ~1.0–2.1 μm thick and appears pseudoreticulate in transmitted light microscopy. Processes are generally stubby and have blunt or furcated tips. Tabulation is expressed by low to moderate sutural septae, and is typical of the genus. Spiniferites multisphaerus sp. nov. has been found in low abundances throughout the Late Quaternary in Guaymas Basin with maximum abundances of 6% or 1670 cysts g−1, and is rare in the Holocene, including modern sediments.