The phylogenetic affiliation and temporal variability in the abundance of planktonic anammox bacteria were studied at a time-series station above the continental shelf off central Chile (~36°S; bottom depth 93m), a wind-driven, seasonal upwelling area, between August 2006 and April 2008. The study was carried out by cloning and sequencing the 16S rRNA gene and by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Our results showed the presence of a single anammox bacteria-like ribotype during both upwelling and non-upwelling seasons, which was phylogenetically associated with a recently described oxygen-minimum-zone subcluster within the Candidatus Scalindua clade. Moreover, clear differences were observed in the temporal and vertical distribution of anammox cells. During the upwelling season (austral spring-summer), relatively high abundances (~5500cellsmL -1) and large cells (0.8μm 3-75.7fgCcell -1) were found below 20m depth. In contrast, during the non-upwelling season (austral fall-winter), lower abundances (~600cellsmL -1) and smaller cells (0.1μm 3-22.8fgCcell -1) were found, predominantly associated with the bottom layer. Overall, our results indicate that the abundance and vertical distribution of anammox planktonic assemblages are related to the occurrence of seasonal, wind-driven, coastal upwelling, which in turn appears to offer favorable conditions for the development of these microorganisms. The dominance of a unique anammox bacteria-like ribotype could be related to the high environmental variability observed in the system, which prevents the establishment of other anammox lineages.