Anthropozoonotic diseases threaten the survival of western lowland gorillas (Gorilla gorilla gorilla). Use of accurate diagnostic techniques in gorilla health monitoring contributes to the conservation of gorillas by providing robust information for appropriate management decisions. To identify suitable protozoa diagnostic techniques for wild gorillas, 95 fecal specimens were collected in Lopé National Park and east of Moukalaba-Doudou National Park in Gabon, areas with high and low levels of human activity, respectively. The samples were examined for Cryptosporidium sp. and Giardia sp. by using the following diagnostic techniques: a commercially available immunofluorescent antibody test kit, Merifluor, and a rapid immune-assay, ImmunoCard STAT!, to detect Cryptosporidium sp. and Giardia sp., and a modified Ziehl-Neelsen stain to detect Cryptosporidium sp. oocysts. The results obtained from the Merifluor test, considered the “gold standard” in human studies, were used to estimate the prevalence of Cryptosporidium sp. and Giardia sp. infections in Lopé National Park (19.0% and 22.6%, respectively) and east of Moukalaba-Doudou National Park (0% and 9.1%, respectively). The difference in prevalence in both areas may be associated with differing levels of anthropogenic disturbance. The sensitivity and specificity of the latter two diagnostic techniques were calculated by using the Merifluor test as a control. The ImmunoCard STAT! was found suitable for Giardia sp. antigen detection (specific but not sensitive) and inappropriate for Cryptosporidium sp. antigen detection (not specific or sensitive). The modified Ziehl-Neelsen stain was found to be highly specific but not sensitive in the detection of Cryptosporidium sp. oocysts. These results underline the necessity of using ancillary tests and concentration methods to correctly identify positive samples. This is the first report of Cryptosporidium sp. and Giardia sp. infections in free-ranging western lowland gorillas and highlights the importance of verifying the accuracy of diagnostic techniques developed for human use before applying these to non-human primates.