This study characterizes the abundance and spatial distribution of siphonophores between the Trinidad Channel (50°06′S) and the Strait of Magellan (52°45′S) in southern Chile, during October–November 2009. Ten species were identified, of which Agalma elegans, Rosacea plicata and Sphaeronectes fragilis are new records for this region. Dominant species showed similar dominance values e.g. Lensia conoidea (26.3%), Dimophyes arctica (24.6%), Lensia meteori (22.2%) and Muggiaea atlantica (20.7%). Eudoxids of L. conoidea and D. arctica represented 97.3% of all eudoxids collected and they were mainly collected in estuarine waters. The highest densities were found in estuarine waters (high vertical stratification and low temperature, salinity and dissolved oxygen values). On the other hand, the lowest densities were found in coastal areas influenced by permanent influx of Sub-Antarctic waters from the Pacific (greater instability and vertical mixing, higher temperatures, salinity and dissolved oxygen values). Temperature and dissolved oxygen were the most important environmental variables. In general, all the dominant species showed a positive association with temperature and a negative association with dissolved oxygen (with the exception of L. meteori). The vertical distribution showed that M. atlantica was mainly distributed in the first 50 m, in association with estuarine waters, while L. conoidea, L. meteori and D. arctica were mainly found in the deeper layer (50–200 m) and in association with modified Sub-Antarctic waters. The comparison of the results obtained in the springs of 1996 and 2009 showed a significant increase in abundance.