Two invasive fish species, the round goby Apollonia melanostoma syn. Neogobius melanostomus (Pallas 1814) and the bighead goby Neogobius kessleri (Günther, 1861), have established a firm population in Austrian waters during the past 15 years. As there have been no records of the parasite fauna from these populations, a total of 79 specimens of A. melanostoma and 12 specimens of N. kessleri were examined for parasites between May and October 2007 from three different sampling sites from the Danube River in Austria. In total 12 parasite taxa were recovered. The protozoans Trichodina sp. and Ichthyophthirius multifiliis from the gills and skin; two crustacean species, Paraergasilus brevidigitus and Ergasilus sieboldi, from the gills; and the two monogeneans Gyrodactylus sp. and Dactylogyrus sp., from the skin and gills respectively, all occurred at low prevalence and intensities. Furthermore, cystacanths of the acanthocephalan Acanthocephalus lucii were found in the body cavity. Metacercariae of the digeneans Diplostomum sp. and Tylodelphys clavata were found in the lens of the eye and the vitreous humour, respectively. Adults of two digeneans, Nicolla skrjabini and Bunodera nodulosa, were found in the intestine. In addition, during this survey metacercariae of the Holarctic digenean Bucephalus polymorphus, encysted in the skin and fins, with prevalence up to 78%, were recorded for the first time in Austria.