Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two domains are relatively unknown. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves, or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. We factorially manipulated both species and intraspecific richness of three diatoms to test effects on biomass production and bacterial diversity of algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community, which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on attached/particle-associated bacterial diversity, or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.