A molecular phylogeny based on 917 base pairs (bp) of the mitochondrial (mt) DNA cytochrome-b gene was used to test and reassess the systematics and conflicting taxonomic treatments of the small, black-and-white Puffinus shearwaters, including the P. assimilis-lherminieri species complex. Three geographically discrete clades were identified in the North Atlantic, Southern (Australasia) and tropical Pacific and Indian oceans that contain most of the P. assimilis-lherminieri taxa. Together with four other lineages (P. puffinus, P. opisthomelas, P. mauretanicus-P. yelkouan, P. newelli-P. myrtae), they form an unresolved polytomy. Puffinus huttoni-P. gavia, P. nativitatis, and P. subalaris are basal to this. The phylogenetic positions of P. myrtae and P. subalaris are unexpected and warrant further investigation. None of the competing taxonomic treatments of the P. assimilis-lherminieri complex are supported. Instead, our phylogeny suggests that 14 taxa should be recognized, whereas five others (loyemilleri, colstoni, nicolae, polynesiae, and atrodorsalis) are phylogenetically undifferentiated from more widespread species (lherminieri, dichrous, and bailloni) and are probably not valid. Similarities in plumage and external morphological characters between unrelated species and differences between closely related species suggest that those traditional taxonomic characters are poor indicators of phylogenetic relatedness.