The bacterial flora of clinically healthy reptiles can be extremely diverse. The objectives of this study were to determine the bacterial flora in oral swabs from two different species of water turtles and to study growth characteristics and antibiotic resistance of these isolates. Oral swabs were collected from 20 clinically healthy common musk turtles (Sternotherus odoratus) and 20 West African mud turtles (Pelusios castaneus) and incubated at two different temperatures (25 and 37°C; 77.0 and 98.6°F) on various agar plates. All isolates were tested for susceptibility to a panel of antibiotics. A total of 66 distinct bacterial types were collected, 63 (95.45%, 95% confidence interval [CI]: 90–100) of which were Gram negative and 3 (4.55%, 95% CI: 0–27) of which were Gram positive. The most commonly isolated genera were Citrobacter spp. (in 97.5% of the animals tested, 95% CI: 93–100), Aeromonas spp. (in 92.5% of the animals tested, 95% CI: 84–100), Chryseobacterium spp. (in 80% of the animals tested, 95% CI: 68–92), and Salmonella spp. (in 80% of the animals tested, 95% CI: 68–92). The most commonly isolated bacterium was Aeromonas hydrophila (77.5%, 95% CI: 65–90). The oral bacterial flora of all of the examined animals consisted of a wide mixture of bacteria, many of which were potential pathogens. The combination of bacteria detected differed between individual animals. Incubation at 25 and 37°C led to the detection of distinct populations of bacteria. The resistance testing showed that many of the bacteria detected were resistant to a wide range of antibiotics.