We performed molecular phylogenetic analyses using nucleotide sequence data from five genes (16S rRNA, cytochrome c oxidase subunit I, 18S rRNA, 28S rRNA, histone H3) determined from 36 specimens representing 25 (10 named, 15 unnamed) species of lineid heteronemerteans collected in Sagami Bay, Japan, along with other sequences obtained from public databases. External features of the 25 species are briefly described and illustrated. Lineus fuscoviridis Takakura, 1898 is transferred to Notospermus Huschke, 1830. Our molecular analysis indicated that one of our Notospermus specimens from Sagami Bay and material previously collected from the Seto Inland Sea are conspecific with Notospermus geniculatus (Delle Chiaje, 1822) s. str. [the year of publication is not 1828 as previously regarded], originally described from Naples, Italy. The new species Siphonenteron nakanoi is established; our tree shows it as the sister taxon to Siphonenteron bilineatum Renier in Meneghini, 1847; it differs from the latter in having more diffuse, scattered yellow pigmentation at the anterolateral margin of the head on each side. Pros and cons of lumping and splitting Lineidae in future studies are discussed.