Aim: Phyllanthus columnaris Müll.Arg. was found to possess anti-methicillin resistant Staphylococcus aureus (antiMRSA) activities. This study aimed at isolating, identifying and evaluating the active compounds from the stem bark of Phyllanthus columnaris Müll.Arg. against MRSA. Methodology and results: Stem bark extracts (methanol, acetone and aqueous) of Phyllanthus columnaris were subjected to anti-MRSA screening by disc diffusion method. MIC and MBC tests were carried out to compare the lowest concentration to inhibit and kill the sixteen MRSA tested among the three extracts. TLC bioautography were performed to detect the bioactive compounds. Isolation of the two active compounds was performed by means of preparative TLC. Morphological and ultra-structure alterations of the MRSA treated with bioactive compounds after 24 h were revealed by scanning and transmission electron microscopy. Both methanol and acetone extracts exhibited good anti-MRSA activity with the lowest minimum inhibitory concentration (MIC) value for both extracts were 0.78 mg/mL and the lowest minimum bactericidal concentration (MBC) were 1.56 mg/mL. Bioassay-guided chromatography by bioautography revealed two active anti-MRSA compounds from both tannin-free methanol and acetone extracts and characterized as stigmasterol and lupeol by nuclear magnetic resonance (NMR) spectral data. Scanning and transmission electron microscopy of MRSA treated with stigmasterol and lupeol showed cell wall disruption, release of cytoplasmic compounds and decreased in cellular volume. Conclusion, significance and impact of study: Results obtained herein, may suggest that the stem bark of Phyllanthus columnaris possess anti-MRSA and the two of the active compounds isolated were stigmasterol and lupeol. Their anti-MRSA effects up to the morphological and ultra-structure studies were not reported earlier