Myrionecta rubra (Lohmann 1908, Jankowski 1976) is a photosynthetic ciliate with a global distribution in neritic and estuarine habitats and has long been recognized to possess organelles of cryptophycean origin. Here we show, using nucleomorph (Nm) small subunit rRNA gene sequence data, quantitative PCR, and pigment absorption scans, that an M. rubra culture has plastids identical to those of its cryptophyte prey, Geminigera cf. cryophila (Taylor and Lee 1971, Hill 1991). Using quantitative PCR, we demonstrate that G. cf. cryophila plastids undergo division in growing M. rubra and are regulated by the ciliate. M. rubra maintained chl per cell and maximum cellular photosynthetic rates (Pmax cell ) that were 6–8 times that of G. cf. cryophila. While maximum chl-specific photosynthetic rates (Pmax chl ) are identical between the two, M. rubra is less efficient at light harvesting in low light (LL) and has lower overall quantum efficiency. The photosynthetic saturation parameter (Ek) was not different between taxa in high light and was significantly higher in M. rubra in LL. Lower Chl:carbon ratios (h), and hence Pmax C rates, in M. rubra resulted in lower growth rates compared with G. cf. cryophila. G. cf. cryophila possessed a greater capacity for synthesizing protein from photosynthate, while M. rubra used 3.2 times more fixed C for synthesizing lipids. Although cryptophyte plastids in M. rubra may not be permanently genetically integrated, they undergo replication and are regulated by M. rubra, allowing the ciliate to function as a phototroph.