Probiotics are live microorganisms that promote the health of their host by producing bioactive metabolites in the digestive tract, where they combat harmful microorganisms. This study aimed to isolate, screen, and identify native probiotics from Clark's clownfish (Amphiprion clarkii). After assessing the morphological characteristics of the isolates, their antimicrobial activity against pathogenic bacteria was evaluated using the well-diffusion method. The biosafety of the isolates was also investigated, focusing on hemolytic activity, antibiotic sensitivity, and the production of lipase and gelatinase enzymes. The selected isolates were then assessed for key probiotic traits, including resistance to acidic conditions, bile salts, and their ability to colonize the host’s intestine. A total of 29 bacterial isolates were obtained from the digestive tract of A. clarkii, with seven showing antimicrobial activity against all the tested pathogenic bacteria. These seven isolates were further evaluated for biosafety, and isolates CS29 and CS18 demonstrated favorable biosafety profiles. Both isolates exhibited strong resistance to acidic pH, simulated gastric juice, and bile salts, as well as high hydrophobicity, aggregation potential, and co-aggregation. Phylogenetic analysis of the 16S rRNA gene sequences revealed that isolates CS29 and CS18 had the highest similarity to Vibrio kanaloae (98.19%) and Vibrio sp. (97.16%), respectively. The results indicate that Vibrio kanaloae CS18 and Vibrio sp. CS29 possess broad antimicrobial activity and the ability to colonize the intestinal tract, suggesting their potential as probiotics for further in vitro study.