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Madagascar is the world's fourth largest island after: Greenland (in the Arctic), New Guinea, and Borneo. Compared to the three tropical zone islands Madagascar is biogeographically more effectively isolated and is hence called an 'Island Continent'. In contrast to the fauna and vascular plants the diatom flora in general, and presumably its endemic taxa were poorly investigated. From 1904 to 2000 a total of 134 diatom taxa had been described from regionally restricted freshwater spot checks made on the the large island. 95 of these were of fossil origin. All type material was collected during the first 50 years of the 20th century. About 20 samples from other parts of the island were collected recently, and only very few of the formerly described endemic taxa have been found again (9). However, 42 extant taxa are described as new for science. Moreover, several hundred cosmopolitan species or zonal elements of the tropics were observed. Altogether some 310 taxa are documented by photographs and are discussed in the text. For a considerable part, these taxa may prove to be new species.Two taxa were not found in recent samples from Madagascar and originate from elsewhere, but they are also described here, because they are similar and may give rise to confusion. As a provisional record the number of new diatom taxa (175) from Madagascar have not been observed elsewhere so far. However, much more diatoms are either difficult to identify or are more or less well known from other continents, in particular from boreo-alpine zones of the northern Hemisphere. A considerable number of species were found, which are rarely recorded in literature, or are described recently only, e.g. from the small genus Craticula.