This study identifies the abundance and spatial distribution of siphonophores collected during spring of 2011 between the Reloncavi Fjord and the Boca del Guafo Passage, in the Chiloe Inland Sea (CIS), Chile. Nine species of siphonophore were identified (three Physonectae and six Calycophorae), of which Agalma elegans, Cordagalma ordinatum and Lensia meteori were recorded for the first time in the waters of the CIS. The dominant species were Muggiaea atlantica (88.0%) and Lensia conoidea (9.5%). The highest occurrence frequency was recorded for M. atlantica (81.2%) and L. conoidea (62.5%). Eudoxids were collected only for M. atlantica (52.1%), L. conoidea (43.7%) and Dimophyes arctica (4.2%). The highest siphonophore densities were found in the northern microbasin (Reloncavi Fjord, Reloncavi and Ancud gulfs), an area characterised by a predominance of estuarine waters (greater vertical stratification, lower temperatures and salinity, and a higher concentration of dissolved oxygen). The vertical distribution patterns showed that M. atlantica is found throughout the water column in the northern microbasin, though with preference for the depths of 0-50m. In the southern microbasin it was distributed mainly in deeper waters (>50m). L. conoidea tends to avoid the surface estuarine layer (0-25m) and is mainly distributed through deeper layers (>25m). The association with environmental variables shows that temperature and dissolved oxygen have a significantly influence over dominant species. Siphonophorae community showed unimodal responses to the environmental gradients and high interspecific variability compared with previous campaigns in the same geographical area.