Parasitoids belonging to Amoebophryidae (Marine ALVeolate Group II or MALV II) infecting dinoflagellates were investigated in Reloncaví Fjord (southern Chile) in the austral summer 2009. Of the 12 dinoflagellate species recorded during monthly sampling, Prorocentrum micans, Dinophysis acuminata, and Phalacroma rotundata were infected by Amoebophrya spp. To assess parasitoid control of host populations, the short-term dynamics of Amoebophrya spp. were followed for 21 d during a bloom of P. micans. Host mortality induced by Amoebophrya spp. (% hosts killed per day) was estimated by dividing prevalence by the generation time of these parasitoids. Parasitism by Amoebophrya spp. was responsible for ~10% of P. micans mortality between 8 and 17 March. The small subunit rDNA genes of individual parasitoids infecting different host cells were sequenced, and like most environmental sequences retrieved from this ecosystem in January and February, all belonged to the MALV II Clade 4. However, as soon as the P. micans bloom was detected, the MALV II genetic composition changed drastically, with the detection of Clades 1, 4 (a different sub-cluster than before), 5, 6, and 12. Our results suggest that different types of parasitoids belonging to Amoebophryidae likely infect dinoflagellates in Reloncaví Fjord, offering the first demonstration of the presence of important genetic diversity in MALV II inhabiting an ecosystem where dinoflagellate hosts are not the usual dominant phytoplanktonic organisms.