Ciliates are extremely versatile single-celled eukaryotes displaying an enormous functional diversity as key elements of food webs. In this study, we found the ciliates in an artisanal backyard Nile tilapia Oreochromis niloticus farm in Oaxaca, Mexico, to describe the diversity and species distribution. Twenty nominal taxa were recorded inhabiting the studied fish farm; only the species Trichodina centrostrigeata was found parasitizing the gills of the cultured Nile tilapia. Most ciliate species recorded here are indicators of α or β mesosaprobic waters, suggesting that bacteriophage taxa dominate ciliate composition. This study represents the first record of ciliate diversity from an aquaculture farm in Mexico.