In this present investigation, the antibacterial activity of Halodule uninervis against seven bacterial pathogens (Bacillus subtilis; Methicillin-Resistant Staphylococcus aureus (MRSA); Staphylococcus aureus, Micrococcus luteus, Escherichia coli; Klebsiella pneumoniae and Pseudomonas aeruginosa) using different solvent extracts was examined. The results showed the highest activity of ethanol leaves extract of Halodule uninervis against Pseudomonas aeruginosa while displaying the lowest activity against Staphylococcus aureus. However, aqueous extract only showed activity against P. aeruginosa. RAPD analysis for P. aeruginosa treated with H. uninervis leaves extract was done. The obtained results showed that leaves extract affected on P. aeruginosa. RAPD analysis displayed two types of polymorphisms in either absence of amplified fragments in the treated strain of P. aeruginosa or induction of new fragments that were disappeared in the untreated bacteria (control).