Abstract: The nucleotide composition and phylogenetic relationship among the species of Phocoenidae and Monodontieae were studied based on the 377 bp sequences of Cyt b gene and the 330 bp sequences of control region (D-loop).For the Cyt b gene, the average nucleotide contents of T, C, A, and G were 29.0%, 28.8%, 27.2% and 15.0%, respectively; it had 109 variable sites, among which 107 were parsimony-informative, with a sequence variability of 28.9%; two singletons and nucleotide substitution mostly occurred at the third position and the transformation was 13.3. For D-loop fragment, the average nucleotide T, C, A and G contents were 35.9%, 21.8%, 32.4% and 9.9%, respectively; 109 variable sites were detected in the eight species, among which 100 were parsimony-informative; the sequence variability was 31.8% and the transformation was 2.4. The phylogenetic trees showed that Neophocaena phocaenoides represented the most basal member of the family, having a most intimate affinity to Monodontieae. The results aslo indicated that the relationships among the taxa Phocoena sinus, P.spinipinnis and Australophocaena dioptrica were intimate.