Objective To explore the mutations and molecular pathogenesis of coagulation factor Ⅸ (F Ⅸ) gene in a pedigree certificate with hemophilia B. Methods　The proband, a 2 years and 4 months old male, was diagnosed as hemophilia B. The clinical feature include repeated skin petechia and hemorrhinia, and the laboratory examination showed APTT 118.3 s, PT 15s, PLT 287 ×109 /L, FⅨ 2.3%. Peripheral blood samples were collected from the proband with hemophilia B and genealogy. Eight coding exons of F Ⅸ gene in the family members were amplified by PCR, and then sequenced by Sanger sequencing. The sequencing results were compared to F Ⅸ gene mutation database. Results　A c.129delG p.Pro44Glnfs*60 in exon 2 of F Ⅸ gene were detected in the proband, five females found as carrier in the pedigrees diagnosis indicated that the proband aunt's fetus did not carry the pathogenic gene. Conclusions　C.129delG p.Pro44Glnfs*60 in F Ⅸ gene is a pathogenic mutation in this pedigree with hemophilia B. Gene diagnosis is helpful to recurrent risk evaluation and prenatal diagnosis.