Purpose: This study was designed to evaluate the molecular genetics of a Chinese family with Bardet-Biedl syndrome (BBS). Methods: All the family members underwent medical history evaluation, ophthalmologic and physical examinations. Whole exome sequencing was performed on two affected individuals and their parents. All variants were verified in all family members by PCR amplification and Sanger sequencing. Results: Patients in this family were diagnosed as Bardet-Biedl syndrome, with an inheritance pattern of autosomal recessive. Compound heterozygous mutations of the FBN3 gene (c.3616G>A and c.6037C>T) were identified by whole exome sequencing. Results from Sanger sequencing showed co-segregation of these compound heterozygous mutations in the FBN3 gene with BBS disease in the family. Conclusion: Novel compound heterozygous mutations c.3616G>A and c.6037C>T of FBN3 were identified in all affected individuals but not in the unaffected family members. This is the first time to the best of our knowledge, that the FBN3 gene is involved in the pathogenesis of BBS. This study will expand our understanding about the gene spectrum related to this genetically heterogeneous disorder.