Objective: To provide effective reference of laboratory detection and prevention-control in avian influenza epidemic via analyzing the detection result of the first case infected avian influenza H5N6 virus in Fujian province. Methods: The viral RNA was extracted from the patient’s throat swab and specimens of surrounding environment, and detected by real-time RT-PCR. The gene sequences of HA and NA gene segments were obtained by RT-PCR and sequencing, the evolution characteristics of the virus were elementarily analyzed by bioinformatics. Results: The avian influenza H5N6 virus was confirmed from the patient’s throat swab, termed influenza A/Fujian-Sanyuan/21099/2017(H5N6)virus. The throat swabs of case from 5 different time points were collected and the H5N6 nucleic acid were detected from the first three times collection. Among 43 specimens of surrounding environment, there were 16 H5 virus samples. The HA and NA gene segments of A/Fujian-Sanyuan/21099/2017 were closely related to A/Cygnus atratus/Hubei/2Z2-O/2016(H5N8) and A/chicken/Hubei/ZYSJF16/2016(H5N6), with a similarity of 99.6% and 99.0% respectively. The cleavage site of HA gene contained multiple basic amino acids. Conclusions The suspected case was the first case infected with avian influenza H5N6 virus in Fujian province, and the HA and NA genes of virus were highly similar to those of H5N8 and H5N6 virus respectively.