Zelleriella ubatubensis, sp. n. is described. This species was found in the caecal region of the leptodactylid Thoropa miliaris from Ubatuba, SP, Brasil. The cell body has an irregular ellipsoid outline (145.9 µm ± 3.0 x 93.9 µm ± 24). The nucleus (16.7 µm ±0.3) has a fragmented nucleolar mass (more than nine nucleoli). Z. ubatubensis seems to be morphologically similar to Z. caryosoma and Z. foliacea but it differs from them by dimension, chromatin and host. A great number of the observed specimens contained Endamoeba paulista in their cytoplasm.