A high-resolution record of organic-walled dinoflagellate cyst production in Guaymas Basin, Gulf of California (Mexico) reveals a complex paleoceanographic history over the last similar to 40 ka. Guaymas Basin is an excellent location to perform high resolution studies of changes in late Quaternary climate and paleo-productivity because it is characterized by high primary productivity, high sedimentation rates, and low oxygen bottom waters. These factors contribute to the deposition and preservation of laminated sediments throughout large portions of the core MD02-2515. In this study, we document dinoflagellate cyst production at a centennial to millennial scale throughout the late Quaternary. Based on the cyst assemblages, three dinoflagellate cyst zones were established and roughly correspond to Marine Isotope Stages (MISs) 1 to 3. MISs 1 and 3 are dominated by cysts of heterotrophic dinoflagellates, whereas MIS 2 is characterized by enhanced variability and a greater proportion of cysts produced by autotrophic taxa. The most dominant dinoflagellate cyst taxa found throughout the core were Brigantedinium spp. and Operculodinium centrocarpum. Dansgaard-Oeschger event 8 is observed in the dinoflagellate cyst record where it is characterized by an increase in warm taxa, such as Spiniferites pachydermus. Other intervals of interest are the Younger Dryas where warmer conditions are recorded and the Holocene which is characterized by the consistent presence of tropical species Stelladinium reidii, Tuberculodinidum vancampoae, Bitectatodinium spongium, and an increase in Quinquecuspis concreta. Changes in cyst assemblages, concentrations, and species diversity, along with geochemical data reflect major orbital to millennial-scale climatic and oceanographic changes.