Cryptosporidium spp. and Giardia duodenalis are parasitic protozoa that can infect various hosts, including humans, domestic animals, and wild animals, making them significant from medical and veterinary perspectives. These protozoa are prevalent in cattle and sheep globally, particularly affecting newborn lambs and calves. This study assessed the occurrence and genetic characteristics of Cryptosporidium spp. and G. duodenalis in asymptomatic lambs and calves under three months in Southeast Türkiye. Fecal samples were collected from 124 animals (69 lambs and 55 calves). A direct immunofluorescence test was used to confirm the presence of G. duodenalis cysts and Cryptosporium spp. oocysts. Molecular confirmation was done with Polymerase chain reaction (PCR) using G. duodenalis SSUrRNA and Cryptosporidium spp. SSUrRNA gene. Microscopic analysis of fecal samples, 17.4% and 43.5% of the 69 lambs, 25.5% and 21.8% of the 55 calves in the study were found to be shedding Cryptosporidium spp. and G. duodenalis oocysts/cysts, respectively. Molecular analysis identified Cryptosporidium species as C. parvum, C. xiaoi, and C. ubiquitum in lambs and C. parvum, C. bovis, and C. ryanae in calves. Assemblages A and E from genotype of G. duodenalis were detected in both lambs and calves. The detection of species and genotypes with zoonotic characteristics in asymptomatic lambs and kids concluded that the Cryptosporidium spp. and G. duodenalis oocysts/cysts shed by lams and calves are important for animal and human health.