A novel endophytic actinomycete, designated strain BSK3Z-2 ^T, was isolated from a surface-sterilised branch of Avicennia mariana from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. Cells were observed to be Gram-stain positive, aerobic, asporogenous and rod-shaped. Strain BSK3Z-2 ^T was found to grow optimally at 30 °C, pH 7.0 and in the presence of 1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BSK3Z-2 ^T belongs to the genus Phycicoccus and has high 16S rRNA gene sequence similarity of 98.1% with Phycicoccus endophyticus IP6SC6^T. Phylogenetic analysis based on the genome of strain BSK3Z-2 ^T was performed by extracting and aligning 39 conserved proteins and 88 housekeeping genes, which further confirmed the phylogenetic assignment of strain BSK3Z-2 ^T. The draft genome of strain BSK3Z-2 ^T is 3.54 Mbp with a DNA G + C content of 73.8%. The average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain BSK3Z-2 ^T and species of genus Phycicoccus were 73.8–85.6%, 64.5–75.9% and 19.5–23.8%, respectively, which are below the standard cut-off values for bacterial species delineation. Strain BSK3Z-2 ^T contains MK-8(H₄) as the dominant menaquinone. The cell wall peptidoglycan contains meso-diaminopimelic acid. The polar lipids profile of strain BSK3Z-2 ^T was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The predominant fatty acids were identified as C_15:0, C_17:0, iso-C_16:0 and C_17:1ω8c. Comparing the phenotypic and phylogenetic features of the strain BSK3Z-2 ^T and related taxa, strain BSK3Z-2 ^T is concluded to represent a novel species of the genus Phycicoccus, for which the name Phycicoccus avicenniae sp. nov. is proposed. The type strain is BSK3Z-2 ^T (= CGMCC 1.18743 ^T = JCM 34335 ^T).