Normal microbiota in the gastrointestinal tract has a mutual relationship with its host. This research aimed to know the morphological diversity of heterotrophic bacteria that live in the gastrointestinal tract of rice field eel and its potency as probiotic. Bacterial isolation has been done by cultivated of the sample in the nutrient agar medium and then observed colonies and cell morphology. Candidate probiotics of isolates were selected based on the capability of starch, protein and lipid hydrolysis, bacterial resistance to acidity and bacterial resistance to antibiotics. The result of this research showed there are 10 isolates and have various colonies’ morphological appearance. All of those isolates consist of 40% cocci, 30% small rod and each 10% long rod, streptococci, and spiral. As many as 8 isolates were gram-positive and 2 isolates was gram-negative. The motility test showed 70% of isolates were motile and 30 % non-motile. The results of casein hydrolysis, starch, and fate indicate that 70% of isolates were able to obtain Hydrolyze casein, that 60% of isolates were able to hydrolyze starch and that none of the isolates were able to obtain hydrolyzed fats. All of the probiotic candidates who were tested in isolation are resistant to all antibiotics tested. Thus, it said that not all discoveries meet the criteria as potential candidates.