The phytoplankton carbon-to-chlorophyll a ratio (C:Chl a) provides a critical link between phytoplankton carbon biomass and chlorophyll a concentration, yet its vertical variability and underlying controls remain poorly constrained in tropical oligotrophic oceans. Here, we integrated community composition, carbon biomass, and chlorophyll a data for picophytoplankton (0.2–2 μm), nanophytoplankton (2–20 μm), and microphytoplankton (20–200 μm) collected from seven depths at 27 stations in the western tropical Pacific Ocean in 2019, with the aim of resolving their vertical distributions and major environmental controls.

Pronounced shifts in phytoplankton composition were observed along the water column and closely tracked vertical gradients in light and nutrient availability. Within the picophytoplankton, Synechococcus was concentrated in the well-lit surface layer, whereas Prochlorococcus and picoeukaryotes were enriched in the lower-light subsurface layer. Among nano-and microphytoplankton, dinoflagellates and cyanobacteria were primarily associated with the oligotrophic upper waters, whereas diatoms occurred more frequently in deeper, nutrient-richer, and lower-light waters. Picophytoplankton dominated both cell abundance and carbon biomass, but numerical dominance did not translate proportionally into carbon contribution. Picoeukaryotes, together with several nano-sized cyanobacteria and diatoms, contributed more to carbon biomass than would be expected from their relative abundance.

These vertical differences in community composition and carbon allocation were further reflected in C:Chl a, which was high in the surface layer and lower in the subsurface layer. Light was the strongest environmental predictor of its vertical variability, while community composition also played an important role: dinoflagellates were associated with elevated surface-layer C:Chl a, whereas Prochlorococcus was an important predictor of subsurface C:Chl a. These findings demonstrate that both water-column structure and phytoplankton community composition must be considered when chlorophyll a is used to estimate phytoplankton carbon biomass in tropical oligotrophic open oceans.