Ducks play an important role in transmitting and maintaining mammalian viruses in nature, and are a reservoir host of many animal viruses. We analyzed the fecal virome of four strains (A, B, C, and D) of ducks living in isolation by using metagenomic analysis. The feces of the ducks tested contained 18 animal virus families. The percentage values of RNA virus reads, compared to the total animal virus reads in each of the four strains were 96.96% (A), 97.30% (B), 98.01 (C), and 67.49% (D), and were mainly from Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Reoviridae. Meanwhile, the minority of DNA virus reads were related to Herpesviridae, Adenoviridae, Iridoviridae, and other, low abundance viral families. The percentage values of Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Herpesviridae reads were not significantly different among strains A, B, and C; however, there were marked differences in the abundance of these reads in strain D. In summary, this study provides an unbiased examination of the viral diversity in the feces of four strains of ducks in specific-pathogen-free periods, and highlights the variation in the percentage of viral families present. These results can be used as a reference for detecting duck viral pathogens and predicting zoonotic potential.