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A Gram-stain-negative, strictly aerobic and motile bacterium, designated as FT89T, was isolated from mangrove sediment in Shenzhen, China. Phylogenetic analysis of strain FT89T was mostly related to Microbaculum marinisediminis, with 16S rRNA gene similarity of 99.66%. The genome size of strain FT89T was 5,065,293 bp and the calculated G+C molar content was 65.90mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) value towards M. marinisediminis yielded 93.86% ANI and 53.2% dDDH. Although the 16S rRNA gene similarity is above 98.7%, the ANI and dDDH values are below the established species delineation thresholds (ANI <95% and dDDH <70%). Here, we confirm that strain FT89T represents a novel species. Phenotypic characterization revealed that cells of strain FT89T were ovoid to rod shaped, measuring 0.3–0.7 µm in width and 0.9–3.2 µm in length. Strain FT89T grew at 20–40 °C (optimum 35 °C) at pH 5.5–9.0 (optimum pH 6.0–7.0) with 0–9% (w/v) NaCl (optimum 1–2%). The cells of strain FT89T contained Q-10, and the major cellular fatty acids were composed of C19:0 cyclo ω8c (41.7%) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) (32.4%). Based on phylogenetic, phenotypic and chemotaxonomic analysis, strain FT89T should represent a novel species of the genus Microbaculum, for which the proposed name is Microbaculum mangrovi FT89T (=MCCC 1K08485T=KCTC 8079T).