Molybdenum (Mo) isotopic data from early Cambrian formations in southern China demonstrate the importance of non-euxinic sediments as a promising archive for coeval seawater Mo records. For the first time, in analogue to noneuxinic, nonskeletal carbonates, we report that the pristine phosphorites also can preserve the ambient fluid, which make the pristine phosphorites a new potential fingerprinting tool to record the coeval paleoseawater. Pristine phosphorite and dolomite samples of two early Cambrian formations in southern China suggest that early Cambrian seawater may have had δ97/95Mo values of at least 1.4‰, similar to modern oceans. Low δ97/95Mo (as low as −0.5‰) values were obtained from reworked phosphorite, but evidence suggests that these are reflecting Mo related to Fe oxyhydroxide minerals rather than the coeval seawater. In contrast, late Precambrian dolomite just below the transition to the Cambrian would indicate a δ97/95Mo of coeval seawater slightly heavier than that of the Mesoproterozoic (0.9‰–1‰ versus 0.8‰), suggesting that oceanic circulation patterns may have been thoroughly reorganized by that time, and may have triggered biological diversification from the Ediacaran to the early Cambrian.