Freshwater amphipods are an important component of freshwater ecosystems and they host diverse parasites. Microsporidians are obligatory intracellular parasites and have been reported from almost all animal phyla with more than 1,500 described species. Considering their wide distribution and diversity, very little is known about them in New Zealand. Here, we aimed at understanding distribution, diversity, and abundance of microsporidians from freshwater amphipod species. We screened more than 2,600 individuals of pooled samples of 12 freshwater amphipod species from 79 locations collected throughout the South and North Islands, by amplifying a partial SSU rRNA region. In particular, the most abundant freshwater amphipod species, Paracalliope species complex, was collected from 60 populations; 46 of them were positive for microsporidian infections with low to high prevalence. In addition, microsporidians were detected from 7 other amphipod species. Among all the microsporidians detected from this study, the genus Dictyocoela was the most common; this genus is the dominant microsporidian taxon in Europe as well. Our Bayesian phylogenetic tree shows that most of the Dictyocoelan species discovered in New Zealand formed a distinct clade, sister to the clade of D. mulleri and D. duebenum, and several minor lineages were closely related to D. cavimanum, species found in Europe. Also, the two unique lineages were discovered from Corophiidae and Talitridae amphipod species. In conclusion, microsporidians are abundant, but previously not studied, microparasites in New Zealand freshwater amphipods, and targeted screening effort would no doubt uncover a greater hidden diversity of parasites.