The genus Chaetogaster belongs to the subfamily Naidinae (Naididae); it includes mostly species of small size and is diverse and abundant in surface coarse sediments in streams. The aim of the present study is to initiate an inventory of lineages (=species) of Chaetogaster in Switzerland. We used 135 specimens collected at 6 sites in 4 streams of 4 cantons. We sequenced the cytochrome c oxidase (COI) gene from all specimens and ITS2 and rDNA 28S from all or several specimens of each lineage that was delimited using COI data, and preserved, for morphological identifications, the anterior part of almost all sequenced specimens. We were able to delimit, based on the calculation of genetic distances and analyses of single-locus data, one lineage for Chaetogaster diaphanus (Gruithuisen, 1828), three within Chaetogaster diastrophus (Gruithuisen, 1828), one for Chaetogaster langi Brestcher, 1896, one for Chaetogaster setosus Svetlov, 1925, and three unidentified Chaetogaster spp. Two lineages of Chaetogaster spp. could correspond to a new morphological group, but this should be confirmed in more specimens. We proposed a new identification key of the nominal species and described the three C. diastrophus lineages and two Chaetogaster spp. as new species. The prospects of the present work are to complete the data of the molecular diversity of this genus in Switzerland and to describe the newly found Chaetogaster species on a molecular/morphological basis.