Mesochaetopterus rogeri sp. nov., a new large chaetopterid polychaete from the Mediterranean Sea, is described. The analyses of partial sequences from the nuclear 18S rRNA (643 bp) and the mitochondrial cytochrome oxidase I (577 bp) genes of representative individuals of all known chaetopterid genera indicated the initial assignment of the new species into Mesochaetopterus. These analyses also supported the monophyly of the family and revealed two well-supported clades: Chaetopterus/Mesochaetopterus and Spiochaetopterus/Phyllochaetopterus. Mesochaetopterus rogeri sp. nov. is close to Mesochaetopterus xerecus, which is redescribed here from newly collected material. Mesochaetopterus rogeri sp. nov. was characterized as follows: (1) two long tentacles with dorsal transversal black bands of alternating widths (sometimes with two additional longitudinal light-brown bands); (2) region A with nine chaetigers (up to 12), with 13-19 modified chaetae in the fourth chaetiger; (3) region B with three flat segments, with accessory feeding organs in the second and third segments; (4) sandy straight tubes, 2.5-m long or more, vertically embedded in the sand. In the Bay of Blanes, M. rogeri sp. nov. occurs between 6- and 9-m deep (but also up to 30-m deep), in a patchy distribution (< 1 individual m-2), with maximum densities in April/June (likely to be the result of recruitment events), and minimum densities in September/November (likely to be a behavioural response to increasing sediment dynamics). Although it was originally thought that M. rogeri sp. nov. could be an introduced species, we argue that it is probably a native of the Mediterranean that has been overlooked by scientists up to now.