Light and electron microscopical studies of sea microbes from the coastal waters of Taiwan have revealed an abundant choanoflagellate fauna from these Western Pacific subtropical waters. A total of 25 loricate (Acanthoecidae), 3 thecate (Salpingoecidae), and 1 naked (Codonosigidae) choanoflagellates were recorded for the 1st time from coastal waters of Taiwan. The Taiwanese loricate choanoflagellate fauna is more similar to that of Japan (20 species in common) than to that of the tropical Indian Ocean (11 species in common).