Close evolutionary relationship of great apes and humans results in overlap of their pathogens. Several infectious diseases, defined as "emerging”, recently appeared as serious threat for great apes. The zoonotic potential of most of the parasites of great apes and humans is expected based on morphological similarity. In protozoans, such approach overestimates zoonotic transmissions. Compared to helminths, gastrointestinal protozoa represent neglected part of parasites communities, despite several advantages for the research focused on zoonotic transmissions. Study is a collaborative effort focused on unicellular parasites of Pan and Gorilla and on the impact of intensity of contact with humans on communities of these parasites. We focus on ciliates (Balantidium), apicomplexans (Cryptosporidium), amoebae (e.g. Entamoeba), flagellates (esp. trichomonads and Giardia), Blastocystis and microsporidia (e.g. Encephalitozoon). These parasites are known to parasitize great apes, but knowledge about their occurrence is lacking any attempt to characterize them better. Expected results will contribute to the general knowledge on the evolution of studied parasites and their host specificity. Moreover, results might positively impact the conservation practices.