Six chaetognath species were determined, all for the first time, in the inner waters between Reloncaví Fjord and Boca del Guafo, Chile. Sagitta tasmanica (85.3%) and Eukrohnia hamata (5.8%) were dominant. Sagitta minima was collected for the first time in the southern channel and fjord region. The largest chaetognath aggregations were found around the Desertores Islands, which create a geographic barrier between two microbasins (north and south) with different oceanographic characteristics. S. decipiens was distributed mostly in the surface layer (0-50 m), whereas E. hamata, S. chilensis, S. minima, and S. enflata were found in deeper waters (50-200 m). The vertical distribution of S. tasmanica was homogeneous; mature, egg-carrying individuals were found at greater depths than those without eggs.