Multiple genetic variants of piscine Cryptosporidium spp. were characterized by next-generation-sequencing, starting from total genomic preparations of fish gastrointestinal scrapings. Molecular taxonomic identifications from NGS data were achieved by BLAST searches using public (NCBI GenBank) and in-house (curated) databases. NGS-based taxonomic identifications were also compared to more conventional analyses based on PCR-Sanger sequencing.</p><p>The objective was to compare the two approaches to resolve the systematics of piscine Cryptosporidium spp. and to resolve multiple infections.