19 pages, 6 figures, 2 tables, supplementary data http://plankt.oxfordjournals.org/content/38/1/64/suppl/DC1 ; We explored the distribution patterns of bacterial and archaeal abundances at the phylum and class level using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), examining the among (across 35 water bodies) and within-lake (intra-annual seasonality) patterns in Patagonia (Argentina). Alphaproteobacteria, Betaproteobacteria and Actinobacteria globally dominated the bacterioplankton, whereas Gammaproteobacteria and Archaea never exceeded 3 and 6% of the community, respectively. The different groups showed seasonality, with simultaneous peaks of all bacterial group absolute abundances during late winter or spring, and with peaks of Archaea during winter, late spring and summer. The bacterial groups presented roughly similar relative abundances in all seasons, whereas Archaea varied in their relative contribution to community structure. Multivariate analyses showed that dissolved organic carbon was an important variable structuring the community at the studied taxonomic resolution (using absolute and relative abundances), in both among and within-lake patterns. The absolute abundance of most bacterial groups was significantly higher in mesotrophic and eutrophic systems than in oligotrophic ones (except Actinobacteria), whereas their relative abundances did not change among trophic states (except Bacteroidetes). The lake grouping obtained from CARD-FISH was consistent with previous work using polymerase chain reaction-denaturing gradient gel electrophoresis data: deep oligotrophic lakes clustered together, whereas small and shallow water bodies grouped separately ; This work was supported by a grant from the Argentinean Funds for Technical and Scientific Investigation (FONCYT, PICT 32732). It was also financed by the Program ’Luis Santalo´ of the National Research Council of Spain and the National Council of Scientific and Technical Research of Argentina (CSICCONICET, PROBA 2007AR0018) ; Peer Reviewed