This study determined the epidemiology and molecular identification of intestinal parasites of domesticated animals slaughtered in Amosun Abattoir, Ibadan, Oyo State, Nigeria, in relation to nature of infection, host type, and sex of host. A total of 150 faecal samples were collected and examined for the eggs of the parasites using parasitological examination (sedimentation and microscopy) and molecular identification (PCR amplification and gel electrophoresis). Descriptive analysis was performed using an SPSS Package and T-testing was used to compare the abundance of parasites in these domesticated animals at p≤0.05. A total of 89 (59.53%) samples were infected, with at least one parasite type in goats (49 [32.67%]) and sheep (40 [26.67%]). Fourteen genera of intestinal parasites were encountered; these include the following: Strongyloides, Eimeria, Haemonchus, Trichostongylus, Taenia, Ascaris, Monezia, Oesophagostomum, Dircocoelum, Nematodius, Enterobius, Fasciola, Trichuris, and Giardia species. The number of single parasitic infections was 41 (88.89%) in goats, while sheep had 32 single infections (85.71%), and for mixed infection there was a prevalence of 26 (11.11%) in goats, while theparasitic prevalence in sheep was 22 (14.29%). The most prevalent parasites in sheep and goats were Strongyloides, Eimeria, and Haemonchus species. Strongyloides had the highest parasite mean intensity in goats (3.76±0.08) and sheep (3.64±0.09), closely followed by Haemonchus (goats; 4.00±0.08, sheep; 3.25± 0.08) and Eimeria (goats; 3.13±0.06, sheep; 4.00± 0.1), while Giardia (goats; 3.00±0.06, sheep; 0.00± 0.00), Nemadius (goats; 2.00±0.04, sheep; 0.00± 0.00), Trichuris (goats; 0.00±0.00, sheep; 2.00± 0.05), Dircocoelum (goats; 1.00±0.02, sheep; 0.00± 0.00), and Enterobius (goats; 1.00±0.02, sheep; 3.25± 0.08) had the lowest mean intensity, occurring in just one of the animals. The mean EPG of host type showed no significant difference, p< 0.05 (p=0.87), in the intensity between sheep and goats. Using the PCR method, only the DNA of Eimeria arloingi from goats was amplified. The intestinal parasites encountered in the domesticated animals slaughtered in Amosun Abattoir pose a zoonotic risk to the human population living in Ibadan and its environs, since the location is the source of its meat supply.