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<em>Rhizophora apiculata</em> (<em>R. apiculata</em>) contains an abundance of biologically active compounds due its special salt-tolerant living surroundings. In this study, the total phenolic content and antioxidant activities of various extract and fractions of stem of <em>R. apiculata</em> were investigated. Results indicated that butanol fraction possesses the highest total phenolic content (181.84 mg/g GAE/g dry extract) with strongest antioxidant abilities. Following <em>in vitro</em> antioxidant activity-guided phytochemical separation procedures, lyoniresinol-3α-<em>O</em>-β-arabinopyranoside (<strong>1</strong>), lyoniresinol-3α-<em>O</em>-β-rhamnoside (<strong>2</strong>), and afzelechin-3-<em>O</em>-L-rhamno-pyranoside (<strong>3</strong>) were separated from the butanol fraction. These compounds showed more noticeable antioxidant activity than a BHT standard in the DPPH, ABTS and hydroxyl radical scavenging assays. HPLC analysis results showed that among different plant parts, the highest content of <strong>1</strong>–<strong>3</strong> was located in the bark (0.068%, 0.066% and 0.011%, respectively). The results imply that the <em>R. apiculata</em> might be a potential source of natural antioxidants and <strong>1</strong>–<strong>3</strong> are antioxidant ingredients in <em>R. apiculata</em>.