Infection of marine dinoflagellates by the parasitic dinoflagellate Amoebophrya spp. plays an important role in population dynamics and carbon flow in marine food webs. It has been extensively reported that Amoebophrya parasitoids occur in temperate coastal areas of the northern hemisphere; however, little is known about their distribution and importance in tropical areas and southern oceans. We used an rRNA-based, fluorescent in situ hybridization assay to detect Amoebophrya spp. infections during the decline of a late-summer dinoflagellate population dominated by Ceratium falcatiforme in a tropical coastal area of the southern Atlantic Ocean subjected to recurrent upwelling-downwelling cycles. Conditions during our survey were typical of downwelling when oligotrophic waters dominate the area. C. falcatiforme was the most infected host, with a prevalence averaging 2% over the study area at the beginning of sampling. At a fixed sampling station monitored over 4 wk, Amoebophrya prevalence escalated from 1 to 7% over a 6 d period, concomitant to a 94% decrease in host cell numbers. Infection by Amoebophrya was estimated to have killed ca. 11% of the host cell population within this period; thus, parasitism was not the main factor behind the C. falcatiforme population decline. Estimates based on biovolume calculations indicate that ca. 6.5% of the carbon in the decaying C. falcatiforme population was transformed into parasitoid dinospores, which became available to tintinnid ciliates that were abundant during our survey. Such a trophic link might be relevant in tropical oligotrophic waters when the system is characterized by a microbial food web structure.