This study describes the spatial distribution and abundance of siphonophores concerning oceanographic variables (temperature, salinity, and dissolved oxygen) in the northern Chilean Patagonian Fjord Ecosystem, from Guafo Passage (43º30'S) to Elefantes Gulf (46º40'S) during the winter of 2012. Twelve species were identified, ten belonging to suborder Calycophorae and two assigned to suborder Physonectae. The species Chelophyes appendiculata and Sphaeronectes gamulini are new records for this study area. Dominant species were Muggiaea atlantica (63.15%), Lensia conoidea (21.85%), and Sphaeronectes koellikeri (9.91%). Species richness showed a negative latitudinal gradient, and the highest densities were found in North Moraleda Channel (5316 ind 1000 m-3) and the lowest in South Moraleda Channel, near Elefantes Gulf (71 ind 1000 m-3). Some species showed a significant and positive association with some oceanographic variables, e.g., M. atlantica showed a positive association with dissolved oxygen, L. conoidea with temperature and negative association with dissolved oxygen, Sphaeronectes fragilis, S. koellikeri, and C. appendiculata showed a positive association with salinity. Eudoxids (sexual reproductive stage) were found for M. atlantica, L. conoidea, and Dimophyes arctica, indicating that the PFE conditions are suitable for some siphonophore species even in winter.