Screening and selecting of indigenous gastrointestinal bacteria and nipah worm feces are very important before being applied as probiotics. Previous studies have isolated 10 bacterial isolates from intestinal and nipah worm feces and their known cellulolytic and proteolytic abilities. The purpose of this study was to determine the pathogenicity of all isolates against nipah worms in vitro and in vivo. Testing of pathogenicity in vitro was carried out on blood agar and DNAse agar, while in vivo testing was carried out by injecting 0.1 ml of bacterial suspension into the nipah worm body which was then cultured for 14 days. The results showed that bacterial isolates NrBF6, NrBF 9 and NrBC4 had indications of being pathogenic because they had hemolysis activity in blood agar medium and lysed DNA on DNAse agar medium. Injection suspension of the third liquid bacteria into the nipah worm body showed that the bacteria NrBF6, NrBF9 and NrBC4 had LD50 at the suspension dose of 10³ bacterial cells for 5, 8 and 20 days, respectively. Symptoms of infection that appeared most dominantly in nipa worms were wounds on the surface of the body, broken body segments and the body looked pale.