Tropical coastal seas are overlooked hotspots of Pseudo-nitzschia diversity.

Pseudo-nitzschia is a globally distributed diatom genus with multiple domoic-acid (DA)-producing species that pose ecological and economic risks. Although tropical waters have recently been hypothesized to host rich Pseudo-nitzschia diversity, their actual diversity, cryptic lineages and toxin-environment relationships remain unclear. Here, we conducted a large-scale summer survey across 65 stations along the Chinese coast of the South China Sea using ITS1 metabarcoding, haplotype network analysis and LC-MS/MS toxin quantification. We identified 50 taxa, including four novel phylotypes and 26 newly recorded in this region, representing the highest richness level documented worldwide. Substantial intraspecific divergence occurred in dominant species, especially P. galaxiae, suggesting a cryptic species complex and ongoing diversification. Dissolved DA (dDA) occurred at 75.4% of stations, with a content of 7.7-351.4 ng L-1. The higher toxin levels coincided with the co-occurrence of several toxigenic species despite their low relative abundance (<0.4% of total Pseudo-nitzschia reads), indicating a collective contribution to toxin accumulation. Temperature was the strongest environmental predictor of community turnover and toxin variation. Both total and toxigenic Pseudo-nitzschia richness decreased with rising temperature; in particular, a temperature range of 25-29°C corresponded to higher diversity and elevated dDA levels. Contrastly when temperature was above 29°C, Pseudo-nitzschia assemblages were dominated by warm-adapted and largely non-toxic taxa such as P. calliantha, corresponding to low dDA levels. Our findings provide comprehensive molecular evidence that tropical coasts are Pseudo-nitzschia diversity hotspots. Temperature-mediated restructuring of communities links Pseudo-nitzschia diversity to toxin dynamics, highlighting potential climate-driven shifts in HAB risk in low-latitude seas.