Little is known about the presence of Cryptosporidium spp. and Giardia duodenalis in Algerian sheep, nor their potential role as zoonotic reservoirs. This study aimed to investigate the occurrence of these two protists in lambs. A total of 83 fecal samples were collected from lambs (< 40 days old) on different 14 farms. Samples were screened for Cryptosporidium spp. and G. duodenalis presence with Immunofluorescence technique (IF). Nested PCR of the small subunit ribosomal RNA (rRNA) gene, followed by restriction fragment length polymorphism (PCR-RFLP) and sequence analyses were used to identify Cryptosporidium species. Then, C. parvum was further subtyped by sequencing the highly polymorphic 60kDa glycoprotein (gp60) gene. For G. duodenalis, nested PCR of the glutamate dehydrogenase (gdh) and triose phosphate isomerase (tpi) genes were applied and then PCR-RFLP was used to determine G. duodenalis assemblages. Cryptosporidium oocysts and Giardia cysts were detected in 36/83 (43%) and 23/83 (28%) of fecal samples, respectively. Of the 21/36 (58%) Cryptosporidium samples that were IF-positive, 16/21 (76%) were identified as C. parvum, and 5/21 (24%) C. ubiquitum. From 15 C. parvum isolates, 2 subtypes were identified within the subtype family IIa including IIaA21G2R1 (3/15) and IIaA13G2R1 (1/15), while IIdA16G1 (11/15) was the only subtype within IId subtype family. Of the 16/23 (69%) G. duodenalis IF-positive samples, the most frequent assemblage was the ruminant-specific assemblage E (10/16), followed by assemblage D (4/16), and A + E mixed assemblages (2/16). This study reports for the first time the identification and genotyping of both Cryptosporidium spp. and Giardia duodenalis from lambs in Algeria. This is also the first description of assemblage D in sheep. The presence of zoonotic C. parvum subtypes (IIa, IId) and C. ubiquitum, as well as G. duodenalis, indicates that sheep could play an important role as a potential reservoir for zoonotic protists.