Extant artiodactyls (even-toed hoofed mammals) are traditionally divided into three main lineages: Suiformes (pigs, peccaries and hippopotamuses), Tylopoda (camels and llamas) and Ruminantia (bovids, deer, tragulids and giraffes). Recent molecular studies have not supported a close relationship between pigs and hippopotamuses, however, instead grouping hippopotamuses with Cetacea (whales, dolphins and porpoises). In this study we have sequenced the complete mitochondrial genome of a tylopod — the alpaca (Lama pacos), the only artiodactyl suborder not previously represented by a complete mitochondrial sequence. This sequence was included in phylogenetic analyses together with the complete mitochondrial protein-coding sequences of other artiodactyls plus two cetaceans. Despite the length of the data set, the relationship between Suina (Suiformes sine Hippopotamidae), Tylopoda and Ruminantia/Hippopotamidae/Cetacea could not be fully resolved, however, a basal position of the alpaca (Tylopoda) relative to the other artiodactyls/cetaceans was unsupported.