Livestock plays a great role in the economic development of smallholder farmers. However, the population of livestock has been affected by diseases such as cryptosporidiosis and giardiasis. Sariaya has a large production of livestock that is being distributed in Quezon Province. Thus, the current study aimed to identify the presence of Cryptosporidium sp. and Giardia sp. in livestock in selected farms of Sariaya, Quezon. Risk factors were also assessed in the present study. A total of 103 collected faecal samples from livestock were subjected to microscopic and molecular detection. Faecal samples were processed through Formalin-Ether Concentration Technique (FECT) and Polymerase Chain Reaction. Microscopy results revealed that 14 out of 103 (13.59%) samples were positive for Giardia with meant intensity of 13 cysts per gram (cpg) of faeces, while molecular detection confirmed that 13 out of 103 (12.62%) had amplified for the target gene of Giardia, tpi, with expected band size of 530 bp. Sequenced samples of G. intestinalis were characterised as assemblages A, B and E. Moreover, pigs showed the highest prevalence (15.91%), while cattle had the highest mean intensity (14 cpg) for Giardia. Cryptosporidium were absent in all the samples. Statistical analysis of the risk factors such as diet, feeding floor, habit, presence of illness and faecal consistency of the animals revealed no significant association (p>0.05) in the presence of Giardia. This study revealed the presence of zoonotic Giardia species in the area; however, future investigation in other possible risk factors such as the season and age is still recommended.