Backgound/Objective: Novel compounds for mitigating globally growing microbial resistance to antibiotics have been recently more actively researched. Triviron is a polycationic amphiphile synthetic compound with a ribonuclease activity and is used as an antiviral in veterinary medicine. Methods: We studied the effect of triviron on the mouse (line Balb/c) fecal bacteriobiome at different time points (0, 5, 25, and 120 h after a single intragastrical administration) by using amplicon sequence diversity of the V3/V4 region of 16S rRNA genes. Results: Most of the operational taxonomic units (OTUs) belonged to Bacillota (1168 OTUs, i.e., 56% of the total number of OTUs in the study) and Bacteroidota (354, i.e., 17%), with the phyla together accounting for more than 90% of the total number of sequence reads. We found changed relative abundance of some bacterial taxa with time, including the dominating Bacteroidota and Bacillota phyla; some of the changes were sex-related, although at the start of the experiment, there were no difference between the sexes in their fecal bacteriobiome composition and structure. Conclusions: The results unequivocally demonstrated that in mice, feces bacterial community structure was affected by a one-time triviron administration, even at the highest hierarchical level of phyla. The finding that the core dominant phyla can be affected, with the effect lasting at least for five days, implies that some major and important functions of the gut microbiota can be affected as well.