Giardia, a flagellated protozoan, is widely distributed in wild rodents. To characterize the presence of Giardia in wild rodents in southern China, this study collected 344 fecal samples from wild rodents in Guangxi, Hunan, and Yunnan provinces. The β-giardin gene (bg) was amplified to identify the presence of Giardia sp. The results showed that 48 samples (13.95%, 48/344) tested positive for Giardia, including three positives for G. duodenalis (assemblage G n = 1, assemblage F n = 2) and 45 positives for G. microti. Among these, Microtus fortis had the highest prevalence at 30.22% (42/139), followed by Apodemus agrarius (7.14%, 3/42). Rattus flavipectus showed a prevalence of 2.56% (1/39), while Bandicota indica had a rate of 5.13% (2/39). The prevalence of Giardia in males (18.27%, 36/197) was slightly higher than in females (8.16%, 12/147). To the best of our knowledge, the present study reported the detection of assemblage F and assemblage G in B. indica for the first time. In addition, G. microti was found exclusively in M. fortis and a few A. agrarius. This study enriches the epidemiological data on Giardia in wild rodents and provides new insights for future research.
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