Objective To identify a potential pathogenic gene mutation among a family with hypertrophic cardiomyopathy (HCM) and atrial fibrillation (AF). Methods Clinical data, family history, ECG, and echocardiogram were collected from the proband as well as family members. Genomic DNA was extracted from blood sample, and a gene panel related to hereditary cardiovascular diseases was detected using next-generation sequencing. Mutation identified in the proband was confirmed by Sanger sequencing in other family members and 100 healthy controls. The potential pathogenicity of the identified mutation was assessed by PolyPhen-2, SIFT and Mutation Taster software. Results Three patients showed clinical symptoms related to the pathology. A novel PRDM16 gene c.3124G>A (p.G1042R) mutation was identified in the proband and several members in this family. However, this mutation was not found in the proband's parent and the healthy controls, so it could be a de novo mutation. This mutation was located in a high evolutionary conservation area among different species. Both conservatism and bioinformatics results indicated that the mutation probably had affected the function of the protein. Conclusion The novel missense mutation of PRDM16 gene c.3124G>A might be the disease-causing gene mutation in this Chinese pedigree with familiar HCM and AF.