The eunicid polychaete Marphysa sanguinea was until recently believed to be a cosmopolitan species, with a distribution ranging from the south-west coast of England to the Pacific coast of America, and New Zealand and Australia in the western Pacific. However, there are many morphological and ecological inter-population differences that render the definitive identification of these numerous populations difficult. The recent designation of a neotype, together with a more detailed morphological description of specimens from the type locality in south-west England, has allowed the concept that M. sanguinea represents a series of cryptic species, to be investigated by examining populations of species previously referred to as Marphysa sanguinea. A new species Marphysa mullawa was described from Moreton Bay Queensland, Australia. In this paper we describe a new species from the western Cape of South Africa which has previously been referred to as ‘Marphysa sanguinea’, using an integrative approach combining morphological data, RAPD-PCR analysis and a study of the sperm ultra-structure. The South African species is a popular bait animal for local sea anglers and is heavily exploited throughout the western Cape. The RAPD-PCR analysis also demonstrates that populations referred to as ‘Marphysa sanguinea’ from other geographical locations studied have distinct genetic pools, providing further evidence that Marphysa sanguinea is not a cosmopolitan species and consists of a suite of cryptic species.