We conducted multinet sampling during winter and summer in the Southern Ocean (Atlantic sector) to investigate the effect of water mass, season and water depth on abundance and species composition of meso- and bathypelagic chaetognaths. Eukrohnia hamata (mean 115 ind. 1,000 m-3) and Sagitta marri (mean 51 ind. 1,000 m-3) were dominant, complemented by E. bathypelagica (mean 19 ind. 1,000 m-3) and E. bathyantarctica (mean 19 ind. 1,000 m-3) below 1,000 m. A further six species were identified, among them the rare bathypelagic species Heterokrohnia fragilis and the subtropical Eukrohnia macroneura that is new to the Antarctic. Water depth and season were the principal determinants of abundance and species composition patterns, indicating vertical seasonal migration and vertical segregation of species. The life cycles of E. hamata and S. marri were studied additionally. Their maturity stages were vertically segregated and prolonged reproductive periods are suggested for both species. © Springer-Verlag 2009.