We investigated novel antibacterial and synergistic activities of isocryptomerin isolated from Selaginella tamariscina. Isocryptomerin showed potent antibacterial activity against Gram-positive and Gram-negative bacterial strains including clinical isolates of antibiotic-resistant species such as methicillin-resistant Staphylococcus aureus (MRSA). Additionally, we further investigated the synergistic activity of isocryptomerin with a conventional antibiotic against MRSA. The result indicated that isocryptomerin had considerable synergistic activity in combination with cefotaxime. In summary, the present study suggests that isocryptomerin may have potential as a novel therapeutic agent for treatment of infectious diseases by not only human pathogenic bacteria but also multidrug-resistant bacteria.