Gorgonian corals of Karimunjawa are impacted by anthropogenic activities, such as increasing high mariculture intensity with consequent eutrophication, overfishing, tourism, sewage, and other pollutant discharge, which result in changes in the microbial community structure. In this study, bacterial communities associated with six species of gorgonian, Viminella sp., Ellisella sp., Antipathes sp., Melithaea sp., Astrogorgia sp, and Junceella sp. from both the Marine Protected Area (MPA) and non-Marine Protected Area (non-MPA) zones were screened for their antipathogenic potential against Urinary Tract Infections (UTIs) pathogens. The selected bacterial isolates were identified and compared for their abundance and diversity between the two zones. 156  bacterial strains were assayed for their prospective antipathogenic compounds against seven UTI pathogens, including Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Streptococcus saptophyticus, Acinetobacter baumannii, Klebsiella pneumonia, Candida albicans. The result showed that 17 of  92 (18.48%) and 6 of 64 (9.37 %) bacterial isolates from MPA and non-MPA, respectively, exhibited antimicrobial activity in at least one UTIs pathogens. Analyzing the gene of 16S rRNA discovered that the 17 isolates of MPA were associated with phyla Actinobacteria, Firmicutes, and Proteobacteria, including Streptomyces zhaozhoue, Nocardiopsis salina, Micrococcus endophyticus, Brevibacterium casei, Micrococcus yunnanensis, Saccharopolyspora coralli, Bacillus paramycoides, Virgibacillus salarius, Oceanobacillus iheyensis, Vibrio alginolyticus. In contrast, only six selected isolates of non-MPA were associated with phyla Actinobacteria and Proteobacteria, including  Nocardiopsis salina, Micrococcus yunnanensis, and Acinetobacter soli. The diversity index (H'), species richness (S), and relative abundance of the MPA zone were higher than that of non-MPA. These results demonstrated that gorgonian octocoral species in the MPA region harbor varied bacteria and propose that many gorgonian-associated bacteria have the prospective for advancing broad-spectrum antibiotics.