A new species of Malacoceros is described from estuarine equatorial waters in Libreville (Gabon, West Africa). During a recent environmental study aimed to assess the urban impact on an estuarine ecosystem near Libreville, the collection of sediment samples from the area was undertaken. The local invertebrate macrofauna had not been previously well studied, and to document the biodiversity, specimens were examined in more detail. A new species of Malacoceros was discovered, occurring in mangrove areas. The new species is described and illustrated in detail, and information on three molecular markers was retrieved and partially used for species delimitation analysis. The new species resembles Malacoceros indicus (Fauvel 1928) described from India but is easily distinguished by a very conspicuous morphological character, the presence of 7–11 large tubercles along the anterior margin of the prostomium. The presence of such conspicuous tubercles has never been observed before in Malacoceros. Maximum likelihood trees for species of Malacoceros and the close genera of Rhynchospio, for which we have data, are also provided. The suitability of characters used for species delimitation in Malacoceros is discussed.