AbstractObjectiveThe human scalp harbours a vast community of microbiotal mutualists. Androgenetic alopecia (AGA), the most common form of hair loss in males, is a multifactorial condition involving genetic predisposition and hormonal changes. The role of microflora during hair loss remains to be understood. After having characterized the scalp microbiota of 12 healthy male subjects and 12 AGA male subjects (D0), the aim of this investigation was to evaluate the capacity of Lindera strychnifolia root extract (LsR) to restore a healthy bacterial and fungal scalp microflora after 83 days (D83) of treatment.Material and methodsThe strategy used was based on high‐throughput DNA sequencing targeting the encoding 16S ribosomal RNA for bacteria and Internal Transcribed Spacer 1 ribosomal DNA for fungi.ResultsTest analysis of relative abundance comparing healthy and AGA subjects showed a significant increase of Cutibacterim acnes (P < 0.05) and Stenotrophomonas geniculata (P < 0.01) in AGA subjects. AGA scalp condition was also associated with a significant (P < 0.05) decrease of Staphylococcus epidermidis relative abundance. A lower proportion of Malassezia genus in samples corresponding to AGA scalps and an increase of other bacterial genera (Wallemia, Eurotium) were also noted. At the species level, mean relative abundance of Malassezia restricta and Malassezia globosa were significantly lower (P < 0.05) in the AGA group. Eighty‐three days of treatment induced a significant decrease in the relative abundance of C. acnes (P < 0.05) and S. geniculata (P < 0.01). S. epidermidis increased significantly (P < 0.05). At the same time, LsR treatment induced a significant increase in the proportion of M. restricta and M. globosa (P < 0.05).ConclusionData from sequencing profiling of the scalp microbiota strongly support a different microbial composition of scalp between control and AGA populations. Findings suggest that LsR extract may be a potential remedy for scalp microbiota re‐equilibrium.