Here, we report the complete nucleotide sequence of the 39 107-bp mitochondrial genome of the yeast Pichia sorbitophila. This genome is closely related to those of Candida parapsilosis and Debaryomyces hansenii, as judged from sequence similarities and synteny conservation. It encodes three subunits of cytochrome oxidase (COX1, COX2 and COX3), three subunits of ATP synthase (ATP6, ATP8 and ATP9), the seven subunits of NADH dehydrogenase (NAD1-6 and NAD4L), the apocytochrome b (COB), the large and small rRNAs and a complete set of tRNAs. Although the mitochondrial genome of P. sorbitophila contains the same core of mitochondrial genes observed in the ascomycetous yeasts, those coding for the RNAse P and the ribosomal protein VAR1p are missing. Moreover, the mtDNA of P. sorbitophila contains several introns in its genes and has the particularity of possessing an intron, which is not linked to any upstream exon.