Turbulence is one of the least investigated environmental factors impacting the ecophysiology of phytoplankton, both at the community and individual species level. Here, we investigated, for the first time, the effect of a turbulence gradient (${\rm{Reynolds\ number}}$, from ${\rm{R}}{{\rm{e}}}_{\rm{\lambda }} = 0$ to ${\rm{R}}{{\rm{e}}}_{\rm{\lambda }} = 360$) on two species of the marine diatom Pseudo-nitzschia and their associated bacterial communities under laboratory conditions. Cell abundance, domoic acid (DA) production, chain formation, and Chl a content of P. fraudulenta and P. multiseries were higher for intermediate turbulence (${\rm{R}}{{\rm{e}}}_{\rm{\lambda }} = 160$ or $240$). DA was detectable only in P. multiseries samples. These observations were supported by transcriptomic analyses results which suggested the turbulence related induction of the expression of the DA production locus, with a linkage to an increased photosynthetic activity of the total metatranscriptome. This study also highlighted a higher richness of the bacterial community associated with the non-toxic strain of P. fraudulenta in comparison to the toxic strain of P. multiseries. Bacillus was an important genus in P. multiseries cultures (relative abundance 15.5%) and its highest abundances coincided with the highest DA levels. However, associated bacterial communities of both Pseudo-nitzschia species did not show clear patterns relative to turbulence intensity.