In order to determine the factors controlling the distribution of planktonic foraminifera as a proxy for reconstruction of paleoenvironments, we present data on live assemblages collected in the Southern Ocean. Plankton tows and hydrographic measurements were taken in the upper 400 m of the water column at different sites in the Ross Sea (site B) and at the Polar Front of the Pacific Ocean (site O) during austral summers from 1998 to 2003. Based on qualitative micropaleontological observations we discriminated between Neogloboquadrina pachyderma dextral (dex) and N. pachyderma sinistral (sin). In addition for N. pachyderma (sin) we distinguished four morphs: the first one (1) has a thickened test and depressed sutures; the second morph (2) is represented by specimens characterized by a subspheric and heavily encrusted test; the third morph (3) has a thin and lobate walled test; the fourth one (4) represent the juvenile stage of N. pachyderma (sin) and is characterized by a smaller average size. The microfauna collected in the Ross Sea (site B) is characterized by the dominance of N. pachyderma (sin) (morphs 1 and 2), whereas low occurrences of Turborotalia quinqueloba, N. pachyderma (dex) and Neogloboquadrina dutertrei were noted in the first 50 m of the water column. The water column at this station is characterized by a marked and shallow stratification and a marked thermocline during the sampling season. At the ocean station (site O), the assemblage shows increasing diversification: T. quinqueloba, G. bulloides, N. pachyderma (dex) and few specimens of Globigerinita uvula characterize the planktonic microfauna. There is a predominance of non-encrusted morphs and juvenile specimens (3 and 4). At this station the mixed surface layer is deeper than in the Ross Sea (60–70 m), the pycnocline and the thermocline less marked. The depth and the intensity of the Deep Chlorophyll Maximum (DCM) influence foraminiferal distribution: N. pachyderma (sin) shows abundance peaks at or just below the DCM while G. bulloides peaks above the DCM. Coiling direction of N. pachyderma seems to be not controlled exclusively by Sea Surface Temperature (SST): probably the two coiling types are genetically different. Results document that diversity of planktonic foraminifera, number of specimens and variations in test morphology are related to regional differences in water properties (temperature, salinity, and DCM depth).