The greenshell mussel Perna canaliculus is the most important species in aquaculture in New Zealand. Mussel energetics and growth rates are subject to the natural variability in phytoplankton biomass and species composition and thus understanding the influence of food type on assimilation efficiency is fundamental to the prediction of mussel production and planning farm management. In this study pulse-chase feeding techniques were used to assess the effect of diet on assimilation efficiencies for nine phytoplankton species including three diatoms Chaetoceros calcitrans, Skeletonema costatum and Thalassiosira sp., and three flagellates Eutreptiella sp., Pyramimonas sp. and Isochrysis galbana, and three dinoflagellates Akashiwo sanguineum, Alexandrium minutum and Gymnodinium catenatum. Assimilation efficiency varied with algal species, but it was significantly higher when mussels were fed dinoflagellates (84.5%) compared with diatoms (61.7%) and flagellates (77.9%). Assimilation efficiency of dinoflagellates and flagellates increased with gut passage time, whereas with a diatom diet, a negative correlation was evident. This finding has implications in understanding and predicting growth rates of mussels (and hence commercial yield) in tandem with natural variability in phytoplankton species composition.