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Background: Parasites of Entamoeba and Cryptosporidium genera, prevalent among various vertebrates such as humans and pigs, pose a zoonotic threat as common protozoan pathogens. This study investigated the prevalence and genetic diversity of Entamoeba and Cryptosporidium species in pigs and wild boars across central and southern Vietnam, to ascertain parasite transmission dynamics. Methods: A total of 113 independent stool samples from 77 pigs and 36 wild boars were analyzed using PCR-based molecular methodologies to detect the presence of Entamoeba spp. and Cryptosporidium spp. The identified species were further characterized through Sanger sequencing, and phylogenetic relationships were analyzed. Results: The study revealed a high prevalence of Entamoeba spp. (62%, n = 70/113) and Cryptosporidium spp. (31%, n = 35/113). Entamoeba suis (57%, n = 40) was predominant, followed by Entamoeba polecki (40%, n = 40) and Entamoeba hartmanni (3%, n = 2). Among Cryptosporidium species, Cryptosporidium scrofarum (89%, n = 31) was the most common, followed by Cryptosporidium suis (11%, n = 4). Wild boars exhibited a higher prevalence of Entamoeba infection compared with domestic pigs ( p = 0.019). Conclusions: The study highlights a high prevalence of Entamoeba and Cryptosporidium, suggesting a potential for zoonotic transmission in Vietnam. Further investigations are necessary to determine the extent to which these parasites in pigs and wild boars contribute to the burden in the human population.