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Phytoplankton community structure in the eastern Equatorial Pacific (EEP) and the Peru upwelling system was determined using ChemTax analysis of pigment data. Photosynthetic efficiencies (Fv : Fm), concentrations of macronutrients, iron (Fe), and the redox proteins flavodoxin (Flv) and ferredoxin (Fd) were used to assess the physiological status of the algal communities with respect to Fe. Diel periodicity in Fv :Fm ratios was observed in Fe-stressed populations of Prochlorococcus and type 4 haptophytes (Phaeocystis) in the EEP with daytime values (0.05-0.30) displaying a distinct noontime minimum. On the Peruvian continental shelf, upwelling of Fe-rich subsurface waters led to massive diatom blooms (reaching chlorophyll a [Chl a] values >45 µg L-1) with near-maximal photosynthetic efficiencies (Fv: Fm >0.6). Assimilation and luxurious uptake of Fe, scavenging processes, and Ekman transport off the shelf break led to rapid decreases in Fe concentration and dramatic shifts in phytoplankton assemblages. The shelf break region was dominated by cryptophyte populations with relatively high photosynthetic competency (Fv:Fm = 0.4-0.5). In this region, subnanomolar Fe concentrations limited further diatom growth. As Fe concentrations decreased offshore, haptophyte (coccolithophorids and Phaeocystis) populations contributed approximately 40-80% toward the total Chl a concentration. Haptophyte populations were Fe stressed, as determined by high Fly indices (Flv [Flv + Fd]-1) and low photosynthetic efficiencies (Fv:Fm ∼0.3). The Flv index was very high in regions where Fe concentrations were <0.2 nmol L-1, but it was 0 when Fe levels were >0.4 nmol L-1. In the Peru upwelling, Fe concentrations between 0.2 and 0.4 nmol L-1 represented a transitional region that marked the threshold switch in community Fd and Flv expression. [ABSTRACT FROM AUTHOR]