ABSTRACT: In the river Traun in Austria, diseased European chub Squalius cephalus were observed for several years. In 2019, an investigation of the condition revealed the presence of several myxozoan species in different tissues, without evidence of other pathogens. The most prevalent and abundant myxozoan parasite in the different organs was Myxobolus ellipsoides ex S. cephalus, a parasite formerly only reported to infect the fin of European chub. To further investigate tissue tropism and molecular data of this parasite, samples from eleven different organs of 13 European chub were collected one year later and examined with various methods: myxospore morphology was assessed by microscopy and compared to the literature. A specific PCR-protocol targeting the 18S rRNA gene of M. ellipsoides ex Squalius cephalus and subsequent sequence analyses detected eleven different 18S variants clustering into two groups. To differentiate M. ellipsoides ex S. cephalus unambiguously from other myxozoan parasites in the tissues, histological methods and in situ hybridization with a species-specific probe targeting the 18S rRNA of the parasite were applied. DNA of M. ellipsoides ex S. cephalus could be detected by PCR in each of the examined fish in at least two of the sampled organs, but not in any blood sample. In two fish, M. ellipsoides ex S. cephalus myxospores were detected in plasmodia in the kidney. Our findings present new data regarding tissue tropism and molecular diversity of M. ellipsoides ex S. cephalus in European chub and provide a basis for further studies investigating possible health impacts by this parasite.