Methicillin-Resistant Staphylococcus aureus (MRSA) is a species of S. Aureus, which shows resistance to the methicillin class of antibiotics. MRSA infection poses significant health problems because it causes severe disease in a vulnerable population and also because effective antibiotics are limited. Therefore, the research to find the new anti-MRSA compound is a necessity. The genome mining approach through Biosynthetic Gene Clusters (BGC) analysis can detect the ability of microbes to produce antibiotics. Thus, the study aimed to screen potential anti-MRSA microbes and predict their BGC. This study used ten microorganisms isolated from mangrove areas in Segara Anakan Cilacap and clinical MRSA 2983 from the Faculty of Medicine, UNSOED. All samples microorganisms were cultivated in starch casein nitrate agar. DNA isolation used Quick-DNA Fungal/Bacterial Miniprep Kit, 16S rRNA gene amplification used 27F and 1492R primers, and DNA amplicons were sequenced by the Sanger sequencing method. BCG prediction of the associated genes used antiSMASH 5.1.2. The results showed that W-5A, P-6B, and W-5B isolates have anti-MRSA activities with inhibition indexes of 0.58; 0.53; and 0.47, respectively. Species identification revealed similarity of W-5A with Streptomyces longisporoflavus strain Moghannam M1, P-6B with Ochrobactrum intermedium LMG 3301, and W-5B with Streptomyces cellulosae strain NBRC 13027. The results of BGC analysis showed that Streptomyces longisporoflavus has one region involved in the synthesis of tetronasin. Ochrobactrum intermedium has one region involved in the synthesis ambactin. Streptomyces cellulosae has eight gene clusters for tiacumicin B, actinorhodin, ulleungmycin, albaflavenone, desferrioxamine B/E, stenothricin, auricin, and prejadomycin productions. These results indicate that the microbes isolated from Segara Anakan Cilacap serve as promising antibacterial producers.