The genus Mammillaria is probably the most species-rich genus in the cactus family. To date, there have been a number of infrageneric classifications of the genus, based largely on morphological data. This study utilized molecular (DNA) sequence data from two chloroplast markers (rpl16 intron and the psbA- trnH intergenic spacer) as part of a cladistic study of the genus. However, in order to allow the choice of a suitable outgroup for Mammillaria an initial study used sequence data from the rpl16 intron to investigate phylogenetic relationships in Tribe Cacteae (to which Mammillaria belongs). The result of that study revealed numerous insights into generic relationships within Tribe Cacteae, for example, demonstrating that the tribe is monophyletic in origin and that a lineage containing Aztekium and Geohintonia forms the earliest lineage in the tribe. This study also revealed that members of tribe Cacteae that possess, tuberculate stems, and dimorphic areoles (with the exception of Ariocarpus) form a well-supported clade that includes Mammillaria, Mammilloydia, Coryphantha, Escobaria, Pelecyphora, Neolloydia and Ortegocactus. Furthermore, members of Ferocactus and Stenocactus represent the most suitable outgroups for a study of Mammillaria.;The phylogenetic study using parsimony and Bayesian analyses of Mammillaria yielded a relatively poorly supported cladogram. In spite of this a number of conclusions could be drawn. It appears unlikely that Mammillaria is monophyletic due to the inclusion of Mammilloydia within a 'core' group of Mammillaria species. Members of Mammillaria from western mainland Mexico, the south-western regions of the USA, and Baja California have a possible close evolutionary relationship with the genera Ortegocactus, Neolloydia, Pelecyphora, Coryphantha and Escobaria. It was also discovered that a small group of Mammillaria species from north Central Mexico have lost the entire rpl16 intron. Such intron deletions are considered extremely rare and thus indicate that members of this group of Mammillaria species form a single clade, and are more closely related than to each other than they are to other species of Mammillaria.