It is well known that the classical river dolphins are not a natural group, but up to now the phylogenetic relationships among them are not very clear because different views have been referred from different studies. In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of the baiji (Lipotes vexillifer), the most endangered cetacean species, and conducted phylogenetic analyses for the classical river dolphins based on data from cetacean mitochondrial genomes available. In our analyses, the classical river dolphins split into two separate lineages, Platanista and Lipotes+(Inia+Pontoporia), having no sister relationship with each other, and the Platanista lineage is always within the odontocete clade instead of having a closer affinity to Mysticeti. The position of the Platanista is more basal, suggesting separate divergence of this lineage well before the other one. The Lipotes has a sister relationship with Inia+pontoporia, and they together formed the sister group to the Delphinoidea. This result strongly supports paraphyly of the classical river dolphins, and the nonplatanistoid river dolphins do represent a monophyletic grouping, with the Lipotidae as the sister taxa to (Iniidae+Pontoporiidae), and is well congruent with the studies based on short interspersed repetitive elements (SINEs).