Nutrient availability limits the growth and capacity for carbon fixation of phytoplankton communities across the vast surface ocean, yet nutrient stress of individual phytoplankton taxa co-occurring in this environment is not well constrained. Here we synthesize available metagenomic datasets with bioassay experimental data from the global ocean, including newly collected from the western North Pacific, to identify nutrient limitation patterns and stress levels of the two abundant picocyanobacteria, Prochlorococcus and Synechococcus. Our results demonstrated that the two lineages experience distinct nutrient stress even inhabiting the same environment. Prochlorococcus was predominantly subject to single limitation by either N or Fe, which occurred in approximately 50% of metagenomic samples, whereas co-/serial N–P limitation was observed in only ~20% of samples. In contrast, Synechococcus more frequently experienced co-/serial limitation involving N-P or N-Fe, accounting for approximately 60% of samples. The two groups also exhibit distinct sensitivities to seasonal nutrient supply dynamics in the subtropical western North Pacific. During winter, reduced N stress and concurrent elevated P stress were observed in Prochlorococcus compared to summer, whereas no significant changes were found in Synechococcus between the two seasons. Overall, our results suggest that nutrient stress in oligotrophic oceans is highly taxon-specific even in the same environment, likely associated with the nutrient acquisition strategies, elemental requirements, and physiological sensitivity to nutrient supply stoichiometry among different clades. These findings highlight the importance of taxon-specific nutrient ecology in shaping picocyanobacteria biogeography and nutrient cycling in the oligotrophic ocean.