The first complete mitochondrial genome sequence for a nemertean, Cephalothrix simula, was determined by conventional and long PCR and sequencing with primer walking methods. This circular genome is 16,296 bp in size and encodes 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) typically found in metazoans. All genes are encoded on H-strand except two tRNAs (trnT and trnP). It differs from those reported for other metazoans, but some gene junctions are shared with those of other protostomes. Structure of the mitochondrial genome of C. simula is mostly concordant with the partial mitochondrial genome known for Cephalothrix rufifrons, but notable differences include three large indel events and transposition of 2 tRNAs. Nucleotide composition of the mitochondrial genome of C. simula is highly A+T biased. The compositional skew is strongly reflected in the codon-usage patterns and the amino acid compositions of the mitochondrial proteins. An AT-rich noncoding region with potential to form stem-loop structures may be involved in the initiation of replication or transcription. Gene adjacencies and phylogenetic analysis based on the 12 concatenated amino acid sequences (except atp8) of mitochondrial protein-coding genes show that the nemertean is close to the coelomate lophotrochozoans, rather than the acoelomate platyhelminths.