Forty-seven free-ranging sea turtles (46- Chelonia mydas, 1- Eretmochelys imbricata) were examined via novel use of an endoscopy combined with a rectal enema to obtain large fecal sample volumes. The cloaca was insufflated using an endoscope, after which the bladder and rectum separated, allowing access to the colon. Environmental conditions and location influenced the performance of the procedure initially, but after several attempts the procedure was successfully initiated. In all cases, fecal samples were obtained, and the animals were released to their respective locations. Fecal sample collection using this approach enhances the ability to obtain diagnostic information and perform other scientific analyses of sea turtles.