A new species of Microgastrinae (Hymenoptera: Braconidae) parasitoid wasp, Microgaster godzilla Fernandez-Triana & Kamino, is described from Japan. From a biological and morphological perspective this is a very unusual species. It represents only the third known microgastrine to be aquatic, and the first one to be found entering the water. The female wasp searches for its hosts, aquatic larvae of Elophila turbata (Lepidoptera: Crambidae), mostly by walking over floating plants, but occasionally diving underwater for several seconds to force the larva out of its case, when it is quickly parasitized (parasitization was always observed above water). The unique searching behaviour of M. godzilla as well as its parasitization of aquatic larvae was filmed and it is presented here. The wasp has simple tarsal claws, which are elongate and strongly curved, similar to those found in the related genus Hygroplitis; they seem to represent an adaptation for gripping to the substrate when entering the water. The new species is described based on morphological, molecular (DNA barcoding), biological and ethological data. Additionally, we provide detailed diagnoses to recognize M. godzilla from all other described species of Microgaster and Hygroplitis in the Palearctic, Nearctic and Oriental regions.