Helobdella bowermani n. sp. is described from specimens collected in fine sediment of open water benthos of Upper Klamath Lake, Klamath County, Oregon. The new species has pale yellow/buff coloration with scattered chromatophore blotches throughout the dorsal surface, lateral extensions or papillae only on the a2 annulus, dorsal medial row of papillae with small papilla on a1 and larger papillae on a2 and a3, and a small oval scute (rarely triangular). Helobdella bowermani n. sp. is morphologically similar to Helobdella atli and Helobdella simplex. Molecular comparison of CO-I sequence data from H. bowermani n. sp. revealed differences of 10.6%–10.8% with Helobdella californica, differences of 12.2%–13.7% with H. atli, and differences of 12.7%–13.2% with H. simplex.