A new species Capitella ambonensis sp. nov. is described from loamy sand sediment of a mangrove habitat on Ambon Island, Indonesia. The species is described primarily based on the distribution of capillary chaetae and hooks. Methylene blue staining pattern was also used to examine the similarity between the material of this study and other species of Capitella. Capitella ambonensis sp. nov. differs from other Capitella species in the form of hooded hooks and the methylene blue staining pattern. A table that lists all Capitella species with their thoracic chaetal formulas is also provided.