The picoplankton (PP) is responsible for major ecosystem functions in most aquatic environments. However, not much is known about the factors that regulate its total abundance and community structure. Using flow cytometry (FC) to detect particles based on their pigments and nucleic-acid content, we described and quantified the photosynthetic pico plankton (PPP) and the heterotrophic bacterioplankton (HB) populations (or groups) composing PP in 32 water bodies located along a trophic and latitudinal gradient in the Argentinean Pata gonia to determine flowcytometrically defined community structures. We set out to identify the environmental variables regulating total PP abundance, group structure and cytometric diversity. We identified a total of 28 different cytometric populations within the HB, 14 of phycoerythrin (PE)-rich picocyanobacteria (Pcy), 8 of phycocyanin (PC)-rich Pcy, and 41 of picoeukaryotes (Peuk) in the different water bodies, with average 3.9 HB and 4.6 PPP groups per water body. We found a strong influence of environmental factors and a less marked effect of latitude on PP structure. HB and PPP abundances decreased towards higher latitudes but their cytometric diversity did not, whereas HB, PCrich Pcy and Peuk abundances together with PPP diversities increased with higher values of chlorophyll a (chl a). The relative contribution of PE-rich Pcy to total Pcy decreased with chl a, whereas the relative contribution of PC-rich Pcy and the number of PC-rich cytometric populations increased with chl a values. Peuk prevailed over Pcy with increasing trophic status and light attenuation, whereas HB prevailed over PPP with increasing trophic status.