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The diversity of testate amoebae has been far less investigated in tropical regions than in temperate regions. This uneven sampling strongly undermines any discussion about the biogeography of testate amoebae. It is therefore critical to explore more intensively the regions of potential interest for biogeographical studies and for which few data are available. Strangely, one of these is the Galapagos archipelago. Although this region has been of central interest for the study of evolution and biogeography, since the time of Charles Darwin only two very incomplete reports currently exist. Ehrenberg (1853) analysed samples collected by Darwin, and Decloître (1973) analysed eight samples from which he described 14 new taxa. In order to investigate this diverse tropical region more thoroughly we collected soil and moss samples from the Galapagos Islands (94 samples covering all habitats on Santa-Cruz Island from the lowlands to mountain Sphagnum peatlands) and mainland Ecuador (36 samples from three sampling locations at 1000, 2000, and 3000 m elevation) and analysed the testate amoeba communities using light microscopy. We compared the diversity of testate amoebae found in these two sets of samples. A total of 225 morphotaxa were identified altogether, of which 98 were observed only in the Galapagos, 75 only in mainland Ecuador, and 52 in both sets of samples. There are potentially 30 new species from the Galapagos and 5 from mainland Ecuador in the material. However, these numbers may have to be increased if detailed morphometrical and molecular analyses can be done on this material.