Flux and taxonomic composition of the diatom assemblage was determined for biweekly sediment traps in the central Gulf of California over a 2-year period. Fluxes and relative abundance of taxa are not significantly different in traps from the eastern side of the Guaymas Basin and the western side of the Carmen Basin, indicating that patterns of diatom production are uniform across the central gulf at all seasons of the year. The annual maximum in diatom flux occurred during the winter season of both years, either as a sustained event over many weeks (1990) or as a series of short blooms (1991–1992). Of the most abundant taxa, only hyalochaete Chaetoceros species showed a clear seasonal cycle, with a flux maximum in the spring of both years. Factor analysis defines five assemblages representing (1) summer and fall conditions of surface stratification and nutrient limitation, (2) winter bloom triggered by onset of strong northwesterly winds, (3) late spring to summer production probably related to sporadic events during periods of weak southeasterly winds, (4) spring 1991 inferred to reflect the distal edge of a coastal upwelling phase, (5) lateral advection of resuspended sediments from the continental shelf, possibly resulting from trapped coastal waves during summer hurricanes and from storms during the 1991–1992 El Niño-Southern Oscillation (ENSO). The diatom data support the inference that subtropical Pacific water penetrates deeper into the gulf during ENSO events. In order to compare the sediment trap record to a sediment core, a second factor analysis was done using only the taxa which are preserved in the sediment and omitting the most abundant taxa, which showed little downcore variation. This produces five factors representing (1) summer-fall low production, (2) early winter bloom, (3) late winter-spring upwelling, (4) ENSO conditions and (5) a late spring-summer assemblage of uncertain significance. Variation of species characterisic of each factor was examined in piston core Atlantis II 125-8 56JPC taken from the oxygen minimum zone in Guaymas Basin. Correlation to nearby Deep Sea Drilling Project Hole 480 indicates that the core penetrates to about 15 ka, with laminated sediments in the Holocene (0–10 ka) and late deglacial (11–13 ka) and massive (nonlaminated) sediments around Younger Dryas time (10–11 ka) and before 13 ka. Downcore variations in the diatom assemblage do not correspond directly to presence of laminations, implying that the processes controlling bottom water oxygen content are not determined by conditions of surface water production. Presence of calcareous nannofossils downcore correlates inversely with two diatom assemblages (ENSO and winter bloom indicators) and not with occurrence of laminations, suggesting that occurrence of calcareous nannofossils in the sediment is at least partly a function of surface water production. Prior to 12 ka, production was lower than at present during all seasons, implying weaker winds throughout the year; subtropical waters extended to the midgulf as they do today during ENSO events. Between 11 and 12 ka, conditions were similar to those of the present, with relatively high winter and spring production resulting from northwesterly winds. ENSO events were still common, although less so than during the preceding period. Younger Dryas time was one of transition with intermediate conditions: a slackening of winter-spring northwesterly winds and reduction of total annual production, and increased occurrence of ENSO conditions. In the early to middle Holocene winter, northwesterlies increased to a maximum, resulting in very high production, but apparently did not persist into spring; subtropical waters mostly disappeared from the gulf. In the late Holocene, northwesterly winds have supported high production during both winter and spring seasons.