Rodents may serve as reservoirs of zoonotic species of Cryptosporidium; however, data frommolecular surveys in support of this hypothesis are still scarce. In this study, we screened faecesand rectal content from murid and cricetid rodents (N = 58) caught around three farms in Zealand,Denmark, for Cryptosporidium spp. by amplicon-based next-generation sequencing (NGS) ofribosomal genes. Selected samples were further examined using nested conventional PCR targetingSSU rRNA, gp60, and actin genes. Cryptosporidium-specific DNA was identified in 40/58(69%) samples, and in 12 (30%) of the 40 positive animals, mixed cryptosporidial infections wereobserved. Cryptosporidium ditrichi was the species most commonly identified, found in 28 (48%) ofthe animals. Cryptosporidium parvum was identified in 4 (7%) of the animals, all of which were coinfectedwith C. ditrichi. The present study is the first to utilize NGS-based screening for Cryptosporidiumspecies in wild rodents. Moreover, it is the first study to provide molecular data onCryptosporidium in rodents sampled in Denmark and to detect DNA of C. ditrichi in Mus musculus,Myodes glareolus, and Microtus agrestis. The NGS approach was successfully applied to yield newknowledge, and the results showed that zoonotic species of Cryptosporidium are common in muridand cricetid rodents in Zealand, Denmark.