Phylum of spiny-headed worms (Acanthocephala) are constituted of the parasites that attack mainly fish and have a complex life cycle that includes intermediate hosts, members of bottom fauna (Ostracoda, Malacostraca and others). With high rates of infestation they can cause fish disease - acanthocephalosis, and thanks to their ability to accumulate heavy metals in high concentrations, they have a role as bioindicators in aquatic ecosystems. The main objectives of the research were: to investigate the distribution and determine spiny headed worms in fish from rivers: Matica, Gacka Like-Novčića and Una. Sampling was conducted over three years (2010, 2011, and 2012.) The basic biometric parameters of fish hosts and basic quantitative parameters of spiny-headed worms infestation were determined: frequency, median intensity of infestation and the minimum and maximum number of parasites. Determination of spiny headed worms was performed with morphological analysis and sequencing of molecular markers (18S rRNA, ITS and COI) amplified in polymerase chain reaction (PCR). Seven species of spiny-headed worms were determined: Echinorhynchus salmonis and Neoechinorhynchus rutili in the rivers Gacka and Matica, Acanthocephalus lucii and Acanthocephalus anguillae in river Novčica, Pomphorhynchus laevis, Pomphorhynchus tereticollis i Dentitruncus truttae in river Una. Great biodiversity of spiny headed worms in these rivers is likely the result of high quality and clean water, necessary for the settlement of different types of crustaceans that are intermediate hosts for spiny headed worms.