Large numbers of many different species of microorganisms live in the oceans. Yet, much remains to be learned about the exact number of species living in various parts of the ocean and the normal microflora of marine animals. There is very little information available in the literature about normal and pathogenic microorganisms of sea turtles. Adult green sea turtles (Chelonia mydas) are herbi-vores, and the feeding habitat is an important factor that determines the incidence and prevalence of microorganisms in the digestive tract. The Environmental Agency, Abu Dhabi performed a health assessment and population studies of green sea turtles that occur off the coast of Ras Al Khaimah, UAE during May 1997. As part of the study, screening of bacteria, fungi and other microscopic organisms were carried out to assess the normal flora in the oro-pharynx and cloaca of sea turtles. Oro-pharyngeal and cloacal swabs were examined from 45 clinically normal green sea turtles including 36 adults (19 females and 17 males) and 9 juveniles. Direct wet preparation from the oro-pharynx showed budding yeast cells (Candida sp), protozoa, diatoms, Chla-mydomonas sp, Cyanobacteria sp, Cristispira sp, Crustacean larvae and various motile bacteria. Direct wet preparation from the clo-aca showed budding Candida cells, diatoms and bacteria. Bacteriology samples were cultured into Zobell agar, sea water agar, sea water broth, MacConkey's agar and thiosulfate citrate bile sucrose agar (TCBS). Mycology samples were cultured into sea water agar, yeast mold agar, potato dextrose agar, peptone yeast agar, Sabouraud's dextrose agar and Sabouraud's chloramphenicol agar. The bacteria isolated from the oro-pharynx were Vibrio alginolyticus, V.fischeri, V. fluvialis, V. vulnificus, V. mimicus, V. hollisae, V. me-taschnikovi, Planococcus sp.and Pseudomonas sp. The bacteria isolated from the cloaca were Vibrio alginolyticus, V. fischeri, V. fluvi-alis, V. vulnificus, V. metaschnikovi and Planococcus sp. Cynobacteria sp and Cristispira sp were seen in direct microscopy, but failed to grow in culture media. The fungi isolated from the oro-pharynx were Candida sp., Candida tropicalis, Alternaria sp., Exophila sp and Rhodotorula rubra. The fungi isolated from the cloaca were different types of Candida sp. and from the carapace and skin lesions were Candida sp, Candida tropicalis, Bipolaris sp. and Rhodotorula rubra. Other unicellular microorganisms detected from the oro-pharynx were Diatoms, Amoeba sp., Chilodonella sp. and Chlamydomonas sp. Multicellular organisms seen are crustacean larvae and amphipods. Faecal samples were examined for the presence of intestinal metazoan eggs. Trematode and Acanthocephala eggs were seen in most cases. Leaches were noticed near the eyelid, cloaca and neck area of some green sea turtles. Amphipods are one of the crustaceans belonging to the class Malacostraca which seen in the oro-pharynx, skin and carapace lesions of sea turtles.