Background: Cryptosporidiosis and giardiasis are significant parasitic diseases shared between humans and domestic animals. Due to the close contact between humans and domestic animals in rural areas, it is important to consider the potential transmission of zoonotic parasites from infected domestic animals to humans. This investigation aimed to determine the prevalence and molecular characteristics ofCryptosporidiumspp. andGiardia duodenalisin domestic animals and villagers.Methods: A total of 116 fecal samples from villagers and 686 fecal samples from domestic animals in Heilongjiang Province, China, were analyzed for two parasites using nested polymerase chain reaction (PCR) targeting various genetic loci and DNA sequence analysis of the PCR products.Results: By sequence analysis of theSSUrRNA gene, the prevalence ofCryptosporidiumin humans was 0.9% (1/116), with one species ofC. parvum(n = 1) detected; among domestic animals, the prevalence was 2.6% (18/686), with five species identified:C. suis(n = 7) andC. scrofarum(n = 7) in pigs,C. meleagridis(n = 1) in chickens,C. andersoni(n = 1) in cattle, andC. canis(n = 2) in foxes.C. parvum and C. caniswere further subtyped as IIdA19G1 and XXa4 on the basis ofgp60gene. RegardingG. duodenalis, based on theSSUrRNA,bg,gdh, andtpigenes, the prevalence in domestic animals was 5.1% (31/608), with three assemblages identified: A (n = 1) in pigs, D (n = 1) in foxes, and E (n = 27) in geese, cattle, pigs, ducks, and sheep, along with mixed infection of A + E (n = 1) in one pig and B + E (n = 1) in one sheep. NoG. duodenaliswas detected in humans (0/116).Conclusions: The present results show that no overlap of subtypes between animals and villagers was found inCryptosporidiumspp. andG. duodenalis, indicating a minor role of domestic animals in infecting humans in this population. However, the presence of zoonotic protozoa in domestic animals highlights the need for special attention to high-risk individuals during close contact with domestic animals.Graphical