Gregarine apicomplexans are micro-eukaryotic parasites that are found in almost every group of terrestrial, freshwater and marine invertebrates (Leander 2008, Desportes & Schrevel 2013). Around 1700 gregarine species have been reported from less than one percent of today's described invertebrate species, leaving a potential gregarine fauna of 99% of the known invertebrates of the world to be discovered. Gregarines have recently received increased attention due to their recognised importance in the understanding of evolution of parasitism in the Apicomplexa (Janouškovec et al. 2019, Mathur et al. 2019). While they infest invertebrates only, they are closely related to notorious causative agents of e.g. Malaria (Plasmodium), Toxoplasmosis (Toxoplasma) and Cryptosporidiosis (Cryptosporidium), which infect humans and livestock. Given their lifestyle and parasite-host relationship (Rueckert et al. 2019), gregarines represent an intermediate step in the transition from photoautotrophs (as represented e.g. by 'chrompodellids' in the marine environment) to the most important eukaryotic pathogens of humans and domestic animals. Gregarine research efforts in the past 15 years have focused on generating phylogentic data beside the morphological description of new species (e.g. Rueckert et al. 2011, Wakeman et al. 2014, Rueckert & Horák 2018), and the first transcriptomic and genomic data have recently been made available (Janouškovec et al. 2019, Mathur et al. 2019) to better understand the evolutionary role of gregarines. One group of gregarines that remains completely underrepresented in any phylogenetic studies is species from freshwater invertebrate hosts. While there are numerous small subunit (SSU) rDNA sequences available for terrestrial and marine gregarines, only a handful of sequences are known from species utilising freshwater hosts.